2DMR | pdb_00002dmr

DITHIONITE REDUCED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.263 (Depositor) 
  • R-Value Work: 
    0.181 (Depositor), 0.165 (DCC) 

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Ligand Structure Quality Assessment 


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

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

Macromolecule Content 

  • Total Structure Weight: 91.18 kDa 
  • Atom Count: 6,120 
  • Modeled Residue Count: 771 
  • Deposited Residue Count: 823 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DMSO REDUCTASE823Rhodobacter capsulatusMutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52675
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGD

Query on PGD


Download:Ideal Coordinates CCD File
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
4MO

Query on 4MO


Download:Ideal Coordinates CCD File
D [auth A]MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
SO2

Query on SO2


Download:Ideal Coordinates CCD File
F [auth A]SULFUR DIOXIDE
O2 S
RAHZWNYVWXNFOC-UHFFFAOYSA-N
O

Query on O


Download:Ideal Coordinates CCD File
E [auth A]OXYGEN ATOM
O
XLYOFNOQVPJJNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.263 (Depositor) 
  • R-Value Work:  0.181 (Depositor), 0.165 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.03α = 90
b = 81.03β = 90
c = 230.04γ = 90
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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