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.

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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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

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

Macromolecules

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 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Kihlken, M.A., Berks, B.C., Hemmings, A.M.

Revision History  

• 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