3PRC

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)

PDB DOI: https://doi.org/10.2210/pdb3PRC/pdb

Classification: PHOTOSYNTHETIC REACTION CENTER
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 1997-07-29 Released: 1998-11-11
Deposition Author(s): Lancaster, C.R.D., Michel, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.178

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB.

Lancaster, C.R., Michel, H.

(1997) Structure 5: 1339-1359

PubMed: 9351808 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(97)00285-2
Primary Citation of Related Structures:
2PRC, 3PRC

PubMed Abstract:
In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In the original structure of the RC from Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined because in the standard RC crystals it was only approximately 30% occupied with ubiquinone-9 (UQ9). We report here the structural characterization of the QB site by crystallographic refinement of UQ9-depleted RCs and of complexes of the RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor stigmatellin in the QB site.

Organizational Affiliation

Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 143.52 kDa
Atom Count: 10,606
Modelled Residue Count: 1,186
Deposited Residue Count: 1,190
Unique protein chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	A [auth C]	336	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07173
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	B [auth L]	273	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	C [auth M]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER	D [auth H]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain R [auth M] SDF format, chain S [auth M] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M]	I [auth L], J [auth L], R [auth M], S [auth M]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain I [auth L] Focus chain J [auth L] Focus chain R [auth M] Focus chain S [auth M] Interactions & Density Focus chain I [auth L] Focus chain J [auth L] Focus chain R [auth M] Focus chain S [auth M]
BPB Query on BPB Download Ideal Coordinates CCD File SDF format, chain K [auth L] SDF format, chain T [auth M] MOL2 format, chain K [auth L] MOL2 format, chain T [auth M]	K [auth L], T [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain K [auth L] Focus chain T [auth M] Interactions & Density Focus chain K [auth L] Focus chain T [auth M]
MQ7 Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain U [auth M] MOL2 format, chain U [auth M]	U [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain U [auth M] Interactions & Density Focus chain U [auth M]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain E [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
NS5 Query on NS5 Download Ideal Coordinates CCD File SDF format, chain V [auth M] MOL2 format, chain V [auth M]	V [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain V [auth M] Interactions & Density Focus chain V [auth M]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain BA [auth H] SDF format, chain L SDF format, chain M [auth L] SDF format, chain X [auth M] SDF format, chain Y [auth M] SDF format, chain W [auth M] MOL2 format, chain AA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain X [auth M] MOL2 format, chain Y [auth M] MOL2 format, chain W [auth M]	AA [auth H] BA [auth H] L M [auth L] W [auth M] AA [auth H], BA [auth H], L, M [auth L], W [auth M], X [auth M], Y [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain L Focus chain M [auth L] Focus chain W [auth M] Focus chain X [auth M] Focus chain Y [auth M] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain L Focus chain M [auth L] Focus chain W [auth M] Focus chain X [auth M] Focus chain Y [auth M]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth M] SDF format, chain Q [auth M] SDF format, chain Z [auth H] SDF format, chain O [auth M] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] MOL2 format, chain Z [auth H] MOL2 format, chain O [auth M]	O [auth M], P [auth M], Q [auth M], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M] Focus chain Z [auth H] Interactions & Density Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M] Focus chain Z [auth H]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain N [auth M] MOL2 format, chain N [auth M]	N [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	D [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.215
R-Value Work: 0.178
R-Value Observed: 0.178
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.5	α = 90
b = 223.5	β = 90
c = 113.6	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
Agrovata	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1998-11-11

Deposition Author(s):

Lancaster, C.R.D.

Michel, H.

Revision History (Full details and data files)

Version 1.0: 1998-11-11
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2011-11-16
Changes: Atomic model
Version 1.4: 2023-08-09
Changes: Database references, Derived calculations, Other, Refinement description

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Help and Resources

3PRC

PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)

The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)