2QJK

Crystal Structure Analysis of mutant rhodobacter sphaeroides bc1 with stigmatellin and antimycin

PDB DOI: https://doi.org/10.2210/pdb2QJK/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Cereibacter sphaeroides
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMD

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.266
R-Value Work: 0.239
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 596.48 kDa
Atom Count: 42,048
Modelled Residue Count: 5,178
Deposited Residue Count: 5,178
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, M A, D, G, J, M, P	428	Cereibacter sphaeroides	Mutation(s): 1 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, N B, E, H, K, N, Q	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, O C, F, I, L, O, R	179	Cereibacter sphaeroides	Mutation(s): 1 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 XA [auth J] SDF format, chain FA [auth D] SDF format, chain GB [auth M] SDF format, chain OA [auth G] SDF format, chain OB [auth P] SDF format, chain W [auth A] MOL2 format, chain XA [auth J] MOL2 format, chain FA [auth D] MOL2 format, chain GB [auth M] MOL2 format, chain OA [auth G] MOL2 format, chain OB [auth P] MOL2 format, chain W [auth A]	FA [auth D] GB [auth M] OA [auth G] OB [auth P] W [auth A] FA [auth D], GB [auth M], OA [auth G], OB [auth P], W [auth A], XA [auth J]	(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 FA [auth D] Focus chain GB [auth M] Focus chain OA [auth G] Focus chain OB [auth P] Focus chain W [auth A] Focus chain XA [auth J] Interactions & Density Focus chain FA [auth D] Focus chain GB [auth M] Focus chain OA [auth G] Focus chain OB [auth P] Focus chain W [auth A] Focus chain XA [auth J]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain DB [auth M] SDF format, chain EB [auth M] SDF format, chain IA [auth E] SDF format, chain JB [auth N] SDF format, chain LA [auth G] SDF format, chain LB [auth P] SDF format, chain MA [auth G] SDF format, chain MB [auth P] SDF format, chain RA [auth H] SDF format, chain SB [auth Q] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth J] SDF format, chain VA [auth J] SDF format, chain Z [auth B] MOL2 format, chain AB [auth K] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth M] MOL2 format, chain EB [auth M] MOL2 format, chain IA [auth E] MOL2 format, chain JB [auth N] MOL2 format, chain LA [auth G] MOL2 format, chain LB [auth P] MOL2 format, chain MA [auth G] MOL2 format, chain MB [auth P] MOL2 format, chain RA [auth H] MOL2 format, chain SB [auth Q] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth J] MOL2 format, chain VA [auth J] MOL2 format, chain Z [auth B]	AB [auth K] CA [auth D] DA [auth D] DB [auth M] EB [auth M] AB [auth K], CA [auth D], DA [auth D], DB [auth M], EB [auth M], IA [auth E], JB [auth N], LA [auth G], LB [auth P], MA [auth G], MB [auth P], RA [auth H], SB [auth Q], T [auth A], U [auth A], UA [auth J], VA [auth J], Z [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AB [auth K] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth M] Focus chain EB [auth M] Focus chain IA [auth E] Focus chain JB [auth N] Focus chain LA [auth G] Focus chain LB [auth P] Focus chain MA [auth G] Focus chain MB [auth P] Focus chain RA [auth H] Focus chain SB [auth Q] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain Z [auth B] Interactions & Density Focus chain AB [auth K] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain DB [auth M] Focus chain EB [auth M] Focus chain IA [auth E] Focus chain JB [auth N] Focus chain LA [auth G] Focus chain LB [auth P] Focus chain MA [auth G] Focus chain MB [auth P] Focus chain RA [auth H] Focus chain SB [auth Q] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain Z [auth B]
ANJ Query on ANJ Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain HB [auth M] SDF format, chain PA [auth G] SDF format, chain PB [auth P] SDF format, chain X [auth A] SDF format, chain YA [auth J] MOL2 format, chain GA [auth D] MOL2 format, chain HB [auth M] MOL2 format, chain PA [auth G] MOL2 format, chain PB [auth P] MOL2 format, chain X [auth A] MOL2 format, chain YA [auth J]	GA [auth D] HB [auth M] PA [auth G] PB [auth P] X [auth A] GA [auth D], HB [auth M], PA [auth G], PB [auth P], X [auth A], YA [auth J]	(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 GA [auth D] Focus chain HB [auth M] Focus chain PA [auth G] Focus chain PB [auth P] Focus chain X [auth A] Focus chain YA [auth J] Interactions & Density Focus chain GA [auth D] Focus chain HB [auth M] Focus chain PA [auth G] Focus chain PB [auth P] Focus chain X [auth A] Focus chain YA [auth J]
SMA Query on SMA Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain FB [auth M] SDF format, chain NA [auth G] SDF format, chain NB [auth P] SDF format, chain V [auth A] SDF format, chain WA [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain FB [auth M] MOL2 format, chain NA [auth G] MOL2 format, chain NB [auth P] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth J]	EA [auth D] FB [auth M] NA [auth G] NB [auth P] V [auth A] EA [auth D], FB [auth M], NA [auth G], NB [auth P], V [auth A], WA [auth J]	STIGMATELLIN A C₃₀ H₄₂ O₇ UZHDGDDPOPDJGM-WPPYOTIYSA-N		Interactions Focus chain EA [auth D] Focus chain FB [auth M] Focus chain NA [auth G] Focus chain NB [auth P] Focus chain V [auth A] Focus chain WA [auth J] Interactions & Density Focus chain EA [auth D] Focus chain FB [auth M] Focus chain NA [auth G] Focus chain NB [auth P] Focus chain V [auth A] Focus chain WA [auth J]
BGL Query on BGL Download Ideal Coordinates CCD File SDF format, chain CB [auth M] SDF format, chain KA [auth G] SDF format, chain QB [auth Q] SDF format, chain S [auth A] SDF format, chain BA [auth D] SDF format, chain TA [auth J] MOL2 format, chain CB [auth M] MOL2 format, chain KA [auth G] MOL2 format, chain QB [auth Q] MOL2 format, chain S [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain TA [auth J]	BA [auth D] CB [auth M] KA [auth G] QB [auth Q] S [auth A] BA [auth D], CB [auth M], KA [auth G], QB [auth Q], S [auth A], TA [auth J]	2-O-octyl-beta-D-glucopyranose C₁₄ H₂₈ O₆ BVHPDIWLWHHJPD-RKQHYHRCSA-N		Interactions Focus chain BA [auth D] Focus chain CB [auth M] Focus chain KA [auth G] Focus chain QB [auth Q] Focus chain S [auth A] Focus chain TA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain CB [auth M] Focus chain KA [auth G] Focus chain QB [auth Q] Focus chain S [auth A] Focus chain TA [auth J]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth L] SDF format, chain JA [auth F] SDF format, chain KB [auth O] SDF format, chain SA [auth I] SDF format, chain TB [auth R] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain KB [auth O] MOL2 format, chain SA [auth I] MOL2 format, chain TB [auth R]	AA [auth C] BB [auth L] JA [auth F] KB [auth O] SA [auth I] AA [auth C], BB [auth L], JA [auth F], KB [auth O], SA [auth I], TB [auth R]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth L] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain SA [auth I] Focus chain TB [auth R] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth L] Focus chain JA [auth F] Focus chain KB [auth O] Focus chain SA [auth I] Focus chain TB [auth R]
SR Query on SR Download Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain IB [auth N] SDF format, chain QA [auth H] SDF format, chain RB [auth Q] SDF format, chain Y [auth B] SDF format, chain ZA [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain IB [auth N] MOL2 format, chain QA [auth H] MOL2 format, chain RB [auth Q] MOL2 format, chain Y [auth B] MOL2 format, chain ZA [auth K]	HA [auth E] IB [auth N] QA [auth H] RB [auth Q] Y [auth B] HA [auth E], IB [auth N], QA [auth H], RB [auth Q], Y [auth B], ZA [auth K]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Focus chain IB [auth N] Focus chain QA [auth H] Focus chain RB [auth Q] Focus chain Y [auth B] Focus chain ZA [auth K] Interactions & Density Focus chain HA [auth E] Focus chain IB [auth N] Focus chain QA [auth H] Focus chain RB [auth Q] Focus chain Y [auth B] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.266
R-Value Work: 0.239
R-Value Observed: 0.239
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 352.291	α = 90
b = 147.396	β = 104.13
c = 160.762	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.

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: 2021-10-20
Changes: Database references, Structure summary
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description