2OZ1 | pdb_00002oz1

The SoxAX Complex of Rhodovulum Sulfidophilum

PDB DOI: https://doi.org/10.2210/pdb2OZ1/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Rhodovulum sulfidophilum
Expression System: Rhodobacter capsulatus
Mutation(s): Yes

Deposited: 2007-02-23 Released: 2008-01-08
Deposition Author(s): Kihlken, M.A., Berks, B.C., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.242 (Depositor), 0.240 (DCC)
R-Value Work:
0.187 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The crystal structure of recombinant Rhodovulum sulfidophilum SoxAX confirms cysteine persulfide coordination to the catalytic heme

Kihlken, M.A., Berks, B.C., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 182.35 kDa
Atom Count: 13,668
Modelled Residue Count: 1,592
Deposited Residue Count: 1,596
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diheme cytochrome c	A, C, E, G	261	Rhodovulum sulfidophilum	Mutation(s): 1 Gene Names: soxA EC: 2.8.5.2
UniProt
Find proteins for Q939U1 (Rhodovulum sulfidophilum) Explore Q939U1 Go to UniProtKB: Q939U1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q939U1
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	B, D, F, H	138	Rhodovulum sulfidophilum	Mutation(s): 0 Gene Names: soxX
UniProt
Find proteins for Q939U4 (Rhodovulum sulfidophilum) Explore Q939U4 Go to UniProtKB: Q939U4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q939U4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain T [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain T [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth G] mmCIF format, chain S [auth G] mmCIF format, chain T [auth H]	I [auth A] J [auth A] K [auth B] L [auth C] M [auth C] I [auth A], J [auth A], K [auth B], L [auth C], M [auth C], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth G], S [auth G], T [auth H]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth G] Focus chain T [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A, C, E, G	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.242 (Depositor), 0.240 (DCC)
R-Value Work: 0.187 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.975	α = 90
b = 102.949	β = 110.22
c = 115.706	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-01-08

Deposition Author(s):

Kihlken, M.A.

Berks, B.C.

Hemmings, A.M.

Revision History (Full details and data files)

Version 1.0: 2008-01-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-13
Changes: Structure summary

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Help and Resources

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The SoxAX Complex of Rhodovulum Sulfidophilum

The crystal structure of recombinant Rhodovulum sulfidophilum SoxAX confirms cysteine persulfide coordination to the catalytic heme

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2