6DC2

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase C301S variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.992 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase.

Wittenborn, E.C.Merrouch, M.Ueda, C.Fradale, L.Leger, C.Fourmond, V.Pandelia, M.E.Dementin, S.Drennan, C.L.

(2018) Elife 7: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbon monoxide dehydrogenase
A, B, C, D
637Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 1 
Gene Names: cooS
EC: 1.2.7.4
Find proteins for Q72A99 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q72A99
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
A, C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
XCC
Query on XCC

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Download CCD File 
A, B, C, D
FE(4)-NI(1)-S(4) CLUSTER
C CLUSTER
Fe4 Ni S4
QGLWBXDZIHZONR-ODZXJFGOAP
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.992 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.790α = 90.00
b = 144.150β = 98.50
c = 123.690γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM069857
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008334

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references