1W5C

Photosystem II from Thermosynechococcus elongatus

PDB DOI: https://doi.org/10.2210/pdb1W5C/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Thermosynechococcus vestitus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2004-08-06 Released: 2004-12-21
Deposition Author(s): Biesiadka, J., Loll, B., Kern, J., Irrgang, K.-D., Saenger, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster

Biesiadka, J., Loll, B., Kern, J., Irrgang, K.-D., Zouni, A.

(2004) Phys Chem Chem Phys 6: 4733

Macromolecule Content

Total Structure Weight: 620.4 kDa
Atom Count: 35,614
Modelled Residue Count: 4,972
Deposited Residue Count: 5,248
Unique protein chains: 10

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM Q(B) PROTEIN 1	A, G	360	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A444 Go to UniProtKB: P0A444
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A444
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II CORE LIGHT HARVESTING PROTEIN	B, H	510	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIQ1 Go to UniProtKB: Q8DIQ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIQ1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II CP43 PROTEIN	C, I	473	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIF8 Go to UniProtKB: Q8DIF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIF8
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II REACTION CENTER D2 PROTEIN	D, J	352	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8CM25 Go to UniProtKB: Q8CM25
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8CM25
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B559 ALPHA SUBUNIT	E, K	84	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIP0 Go to UniProtKB: Q8DIP0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIP0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME B559 BETA SUBUNIT	F, L	44	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIN9 Go to UniProtKB: Q8DIN9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIN9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE	M [auth O], N [auth P]	179	Thermosynechococcus vestitus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYSTEM II 12 KDA EXTRINSIC PROTEIN	O [auth S], Q [auth U]	100	Thermosynechococcus vestitus	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C-550	P [auth T], R [auth V]	163	Thermosynechococcus vestitus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A386 Go to UniProtKB: P0A386
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A386
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
UNASSIGNED SUBUNITS	S [auth X], T [auth Y]	359	Thermosynechococcus vestitus	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA Query on CLA Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain AC [auth H] SDF format, chain AD [auth J] SDF format, chain BB [auth C] SDF format, chain BC [auth H] SDF format, chain CB [auth C] SDF format, chain CC [auth H] SDF format, chain CD [auth J] SDF format, chain DB [auth C] SDF format, chain DC [auth H] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain EC [auth H] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain FC [auth H] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain GC [auth H] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain HC [auth H] SDF format, chain IA [auth B] SDF format, chain IC [auth H] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain JC [auth H] SDF format, chain KA [auth B] SDF format, chain KC [auth H] SDF format, chain LA [auth B] SDF format, chain LC [auth H] SDF format, chain MA [auth B] SDF format, chain MC [auth H] SDF format, chain NA [auth B] SDF format, chain NB [auth G] SDF format, chain NC [auth I] SDF format, chain OA [auth B] SDF format, chain OB [auth G] SDF format, chain OC [auth I] SDF format, chain PA [auth B] SDF format, chain PB [auth G] SDF format, chain PC [auth I] SDF format, chain QA [auth B] SDF format, chain QC [auth I] SDF format, chain RA [auth B] SDF format, chain RB [auth G] SDF format, chain RC [auth I] SDF format, chain SA [auth B] SDF format, chain SC [auth I] SDF format, chain TA [auth B] SDF format, chain TC [auth I] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UC [auth I] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain VC [auth I] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain WC [auth I] SDF format, chain XA [auth C] SDF format, chain XB [auth H] SDF format, chain XC [auth I] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain YB [auth H] SDF format, chain YC [auth I] SDF format, chain ZA [auth C] SDF format, chain ZB [auth H] SDF format, chain ZC [auth I] MOL2 format, chain AB [auth C] MOL2 format, chain AC [auth H] MOL2 format, chain AD [auth J] MOL2 format, chain BB [auth C] MOL2 format, chain BC [auth H] MOL2 format, chain CB [auth C] MOL2 format, chain CC [auth H] MOL2 format, chain CD [auth J] MOL2 format, chain DB [auth C] MOL2 format, chain DC [auth H] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain EC [auth H] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain GC [auth H] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain HC [auth H] MOL2 format, chain IA [auth B] MOL2 format, chain IC [auth H] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain JC [auth H] MOL2 format, chain KA [auth B] MOL2 format, chain KC [auth H] MOL2 format, chain LA [auth B] MOL2 format, chain LC [auth H] MOL2 format, chain MA [auth B] MOL2 format, chain MC [auth H] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth G] MOL2 format, chain NC [auth I] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth G] MOL2 format, chain OC [auth I] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth G] MOL2 format, chain PC [auth I] MOL2 format, chain QA [auth B] MOL2 format, chain QC [auth I] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth G] MOL2 format, chain RC [auth I] MOL2 format, chain SA [auth B] MOL2 format, chain SC [auth I] MOL2 format, chain TA [auth B] MOL2 format, chain TC [auth I] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UC [auth I] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain VC [auth I] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain WC [auth I] MOL2 format, chain XA [auth C] MOL2 format, chain XB [auth H] MOL2 format, chain XC [auth I] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth H] MOL2 format, chain YC [auth I] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth H] MOL2 format, chain ZC [auth I]	AB [auth C] AC [auth H] AD [auth J] BB [auth C] BC [auth H] AB [auth C], AC [auth H], AD [auth J], BB [auth C], BC [auth H], CB [auth C], CC [auth H], CD [auth J], DB [auth C], DC [auth H], EA [auth B], EB [auth C], EC [auth H], FA [auth B], FB [auth C], FC [auth H], GA [auth B], GB [auth C], GC [auth H], HA [auth B], HB [auth D], HC [auth H], IA [auth B], IC [auth H], JA [auth B], JB [auth D], JC [auth H], KA [auth B], KC [auth H], LA [auth B], LC [auth H], MA [auth B], MC [auth H], NA [auth B], NB [auth G], NC [auth I], OA [auth B], OB [auth G], OC [auth I], PA [auth B], PB [auth G], PC [auth I], QA [auth B], QC [auth I], RA [auth B], RB [auth G], RC [auth I], SA [auth B], SC [auth I], TA [auth B], TC [auth I], U [auth A], UA [auth C], UC [auth I], V [auth A], VA [auth C], VC [auth I], W [auth A], WA [auth C], WC [auth I], XA [auth C], XB [auth H], XC [auth I], Y [auth A], YA [auth C], YB [auth H], YC [auth I], ZA [auth C], ZB [auth H], ZC [auth I]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AB [auth C] Focus chain AC [auth H] Focus chain AD [auth J] Focus chain BB [auth C] Focus chain BC [auth H] Focus chain CB [auth C] Focus chain CC [auth H] Focus chain CD [auth J] Focus chain DB [auth C] Focus chain DC [auth H] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain EC [auth H] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain FC [auth H] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain GC [auth H] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth H] Focus chain IA [auth B] Focus chain IC [auth H] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain JC [auth H] Focus chain KA [auth B] Focus chain KC [auth H] Focus chain LA [auth B] Focus chain LC [auth H] Focus chain MA [auth B] Focus chain MC [auth H] Focus chain NA [auth B] Focus chain NB [auth G] Focus chain NC [auth I] Focus chain OA [auth B] Focus chain OB [auth G] Focus chain OC [auth I] Focus chain PA [auth B] Focus chain PB [auth G] Focus chain PC [auth I] Focus chain QA [auth B] Focus chain QC [auth I] Focus chain RA [auth B] Focus chain RB [auth G] Focus chain RC [auth I] Focus chain SA [auth B] Focus chain SC [auth I] Focus chain TA [auth B] Focus chain TC [auth I] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UC [auth I] Focus chain V [auth A] Focus chain VA [auth C] Focus chain VC [auth I] Focus chain W [auth A] Focus chain WA [auth C] Focus chain WC [auth I] Focus chain XA [auth C] Focus chain XB [auth H] Focus chain XC [auth I] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain YB [auth H] Focus chain YC [auth I] Focus chain ZA [auth C] Focus chain ZB [auth H] Focus chain ZC [auth I]
PHO Query on PHO Download Ideal Coordinates CCD File SDF format, chain BD [auth J] SDF format, chain IB [auth D] SDF format, chain QB [auth G] SDF format, chain X [auth A] MOL2 format, chain BD [auth J] MOL2 format, chain IB [auth D] MOL2 format, chain QB [auth G] MOL2 format, chain X [auth A]	BD [auth J], IB [auth D], QB [auth G], X [auth A]	PHEOPHYTIN A C₅₅ H₇₄ N₄ O₅ CQIKWXUXPNUNDV-RCBXBCQGSA-N		Interactions Focus chain BD [auth J] Focus chain IB [auth D] Focus chain QB [auth G] Focus chain X [auth A]
PL9 Query on PL9 Download Ideal Coordinates CCD File SDF format, chain DD [auth J] SDF format, chain KB [auth D] MOL2 format, chain DD [auth J] MOL2 format, chain KB [auth D]	DD [auth J], KB [auth D]	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE C₅₃ H₈₀ O₂ FKUYMLZIRPABFK-UHFFFAOYSA-N		Interactions Focus chain DD [auth J] Focus chain KB [auth D]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain GD [auth T] SDF format, chain HD [auth V] MOL2 format, chain GD [auth T] MOL2 format, chain HD [auth V]	GD [auth T], HD [auth V]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain GD [auth T] Focus chain HD [auth V]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain ED [auth L] SDF format, chain LB [auth E] MOL2 format, chain ED [auth L] MOL2 format, chain LB [auth E]	ED [auth L], LB [auth E]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain ED [auth L] Focus chain LB [auth E]
BCR Query on BCR Download Ideal Coordinates CCD File SDF format, chain FD [auth L] SDF format, chain MB [auth F] MOL2 format, chain FD [auth L] MOL2 format, chain MB [auth F]	FD [auth L], MB [auth F]	BETA-CAROTENE C₄₀ H₅₆ OENHQHLEOONYIE-JLTXGRSLSA-N		Interactions Focus chain FD [auth L] Focus chain MB [auth F]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain VB [auth G] MOL2 format, chain CA [auth A] MOL2 format, chain VB [auth G]	CA [auth A], VB [auth G]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain VB [auth G]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain DA [auth A] SDF format, chain SB [auth G] SDF format, chain TB [auth G] SDF format, chain UB [auth G] SDF format, chain WB [auth G] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain SB [auth G] MOL2 format, chain TB [auth G] MOL2 format, chain UB [auth G] MOL2 format, chain WB [auth G] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth A] DA [auth A] SB [auth G] TB [auth G] AA [auth A], BA [auth A], DA [auth A], SB [auth G], TB [auth G], UB [auth G], WB [auth G], Z [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth A] Focus chain SB [auth G] Focus chain TB [auth G] Focus chain UB [auth G] Focus chain WB [auth G] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.517	α = 90
b = 224.612	β = 90
c = 305.632	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing
SHARP	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-12-21
Type: Initial release
Version 1.1: 2012-08-08
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
Version 1.2: 2014-01-08
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

1W5C

Photosystem II from Thermosynechococcus elongatus

Crystal Structure of Cyanobacterial Photosystem II at 3.2 A Resolution: A Closer Look at the Mn- Cluster

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

Sequence Annotations

Entity ID: 8

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)