3DMR | pdb_00003dmr

STRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0

• PDB DOI: https://doi.org/10.2210/pdb3DMR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodobacter capsulatus
• Mutation(s): No 


• Deposited: 1997-04-25 Released: 1998-03-18 
• Deposition Author(s): Mcalpine, A.S., Bailey, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor) 
• R-Value Work: 
  0.181 (Depositor), 0.218 (DCC) 

Literature

Molybdenum Active Centre of Dmso Reductase from Rhodobacter Capsulatus: Crystal Structure of the Oxidised Enzyme at 1.82-A Resolution and the Dithionite-Reduced Enzyme at 2.8-A Resolution

Mcalpine, A.S., Mcewan, A.G., Shaw, A., Bailey, S.

(1997) J Biol Inorg Chem 2: 690

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 91.13 kDa 
• Atom Count: 6,536 
• Modeled Residue Count: 779 
• Deposited Residue Count: 823 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DMSO REDUCTASE	A	823	Rhodobacter capsulatus	Mutation(s): 0  EC: 1.7.2.3 (UniProt), 1.8.5.3 (UniProt)
UniProt
Find proteins for Q52675 (Rhodobacter capsulatus) Explore Q52675  Go to UniProtKB:  Q52675

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGD	B [auth A], C [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C20 H24 N10 O13 P2 S2 SOFMTHSWCZNJTQ-ILXWUORBSA-N
6MO	D [auth A]	MOLYBDENUM(VI) ION Mo HCNGUXXTNNIKCQ-UHFFFAOYSA-N
O	E [auth A], F [auth A]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor) 
• R-Value Work:  0.181 (Depositor), 0.218 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.45	α = 90
b = 80.45	β = 90
c = 229.11	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-18 
Deposition Author(s): Mcalpine, A.S., Bailey, S.

Revision History  

• Version 1.0: 1998-03-18
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-05-22
  Changes: Data collection