2QJP

Crystal structure of wild type rhodobacter sphaeroides with stigmatellin and antimycin inhibited

PDB DOI: https://doi.org/10.2210/pdb2QJP/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Cereibacter sphaeroides
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2007-07-08 Released: 2007-12-25
Deposition Author(s): Esser, L., Xia, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.277
R-Value Work: 0.244
R-Value Observed: 0.244

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 397.6 kDa
Atom Count: 28,227
Modelled Residue Count: 3,452
Deposited Residue Count: 3,452
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b	A, D, G, J	428	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: petB, fbcB Membrane Entity: Yes
UniProt
Find proteins for Q02761 (Cereibacter sphaeroides) Explore Q02761 Go to UniProtKB: Q02761
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02761
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c1	B, E, H, K	256	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: fbcC Membrane Entity: Yes
UniProt
Find proteins for Q02760 (Cereibacter sphaeroides) Explore Q02760 Go to UniProtKB: Q02760
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02760
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	C, F, I, L	179	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: petA, fbcF EC: 1.10.2.2 Membrane Entity: Yes
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides) Explore Q02762 Go to UniProtKB: Q02762
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02762
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LOP Query on LOP Download Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain Q [auth A] SDF format, chain TA [auth J] SDF format, chain Y [auth D] MOL2 format, chain JA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth J] MOL2 format, chain Y [auth D]	JA [auth G], Q [auth A], TA [auth J], Y [auth D]	(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE C₃₅ H₆₈ N O₈ P FUUNMZKPCMPCHT-ILGKRYBBSA-N		Interactions Focus chain JA [auth G] Focus chain Q [auth A] Focus chain TA [auth J] Focus chain Y [auth D] Interactions & Density Focus chain JA [auth G] Focus chain Q [auth A] Focus chain TA [auth J] Focus chain Y [auth D]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain MA [auth H] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain QA [auth J] SDF format, chain RA [auth J] SDF format, chain T [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain WA [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain T [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth K]	CA [auth E] GA [auth G] HA [auth G] MA [auth H] N [auth A] CA [auth E], GA [auth G], HA [auth G], MA [auth H], N [auth A], O [auth A], QA [auth J], RA [auth J], T [auth B], V [auth D], W [auth D], WA [auth K]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain CA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain T [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain WA [auth K] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain T [auth B] Focus chain V [auth D] Focus chain W [auth D] Focus chain WA [auth K]
ANJ Query on ANJ Download Ideal Coordinates CCD File SDF format, chain KA [auth G] SDF format, chain R [auth A] SDF format, chain UA [auth J] SDF format, chain Z [auth D] MOL2 format, chain KA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain UA [auth J] MOL2 format, chain Z [auth D]	KA [auth G], R [auth A], UA [auth J], Z [auth D]	(2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE C₂₈ H₄₀ N₂ O₉ UPHOMQADKXDOFD-UKHQZXFMSA-N		Interactions Focus chain KA [auth G] Focus chain R [auth A] Focus chain UA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain KA [auth G] Focus chain R [auth A] Focus chain UA [auth J] Focus chain Z [auth D]
SMA Query on SMA Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain P [auth A] SDF format, chain SA [auth J] SDF format, chain X [auth D] MOL2 format, chain IA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth J] MOL2 format, chain X [auth D]	IA [auth G], P [auth A], SA [auth J], X [auth D]	STIGMATELLIN A C₃₀ H₄₂ O₇ UZHDGDDPOPDJGM-WPPYOTIYSA-N		Interactions Focus chain IA [auth G] Focus chain P [auth A] Focus chain SA [auth J] Focus chain X [auth D] Interactions & Density Focus chain IA [auth G] Focus chain P [auth A] Focus chain SA [auth J] Focus chain X [auth D]
BGL Query on BGL Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth G] SDF format, chain M [auth A] SDF format, chain OA [auth J] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth J]	AA [auth E], EA [auth G], M [auth A], OA [auth J]	2-O-octyl-beta-D-glucopyranose C₁₄ H₂₈ O₆ BVHPDIWLWHHJPD-RKQHYHRCSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth G] Focus chain M [auth A] Focus chain OA [auth J] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth G] Focus chain M [auth A] Focus chain OA [auth J]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain NA [auth I] SDF format, chain U [auth C] SDF format, chain XA [auth L] MOL2 format, chain DA [auth F] MOL2 format, chain NA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain XA [auth L]	DA [auth F], NA [auth I], U [auth C], XA [auth L]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain NA [auth I] Focus chain U [auth C] Focus chain XA [auth L] Interactions & Density Focus chain DA [auth F] Focus chain NA [auth I] Focus chain U [auth C] Focus chain XA [auth L]
SR Query on SR Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth G] SDF format, chain LA [auth H] SDF format, chain PA [auth J] SDF format, chain S [auth B] SDF format, chain VA [auth K] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain PA [auth J] MOL2 format, chain S [auth B] MOL2 format, chain VA [auth K]	BA [auth E] FA [auth G] LA [auth H] PA [auth J] S [auth B] BA [auth E], FA [auth G], LA [auth H], PA [auth J], S [auth B], VA [auth K]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth G] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain S [auth B] Focus chain VA [auth K] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth G] Focus chain LA [auth H] Focus chain PA [auth J] Focus chain S [auth B] Focus chain VA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.277
R-Value Work: 0.244
R-Value Observed: 0.244
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.061	α = 90
b = 146.52	β = 110.21
c = 141.003	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Esser, L.

Xia, D.

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary