1UBR

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.121 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Studies of the Carbon Monoxide Complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: Suggestion for the Initial Activation Site for Dihydrogen

Ogata, H.Mizoguchi, Y.Mizuno, N.Miki, K.Adachi, S.Yasuoka, N.Yagi, T.Yamauchi, O.Hirota, S.Higuchi, Y.

(2002) J.Am.Chem.Soc. 124: 11628-11635

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound ...

    The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.


    Organizational Affiliation

    Division of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase Small subunit
S
267Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydA
EC: 1.12.2.1
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21853
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFe] hydrogenase Large subunit
L
534Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: hydB
EC: 1.12.2.1
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21852
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FNE
Query on FNE

Download SDF File 
Download CCD File 
L
(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
C3 Fe Ni O3 S
RSNJUOPWNIKDNA-LMILJAESAR
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
L
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.121 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 98.080α = 90.00
b = 126.010β = 90.00
c = 66.570γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance