6RU9

THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491A VARIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.36 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase

Zacarias, S.Temporao, A.del Barrio, M.Fourmond, V.Leger, C.Matias, P.M.Pereira, I.A.C.

(2019) ACS Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase, small subunitA283Desulfovibrio vulgaris str. HildenboroughMutation(s): 0 
Gene Names: hysBDVU_1917
EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS4 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS4 
Go to UniProtKB:  Q72AS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containingB492Desulfovibrio vulgaris str. HildenboroughMutation(s): 1 
Gene Names: hysADVU_1918
EC: 1.12.7.2
UniProt
Find proteins for Q72AS3 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q72AS3 
Go to UniProtKB:  Q72AS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72AS3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ML
Query on 6ML

Download Ideal Coordinates CCD File 
F [auth A]oxygen-damaged SF4
Fe4 O2 S4
DCVJTSMMUVGUAG-UHFFFAOYSA-M
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
G [auth B]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
H [auth B]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
I [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.445α = 90
b = 98.664β = 105.36
c = 63.885γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BBB-BEP/2885/2014
Fundacao para a Ciencia e a TecnologiaPortugalSFRH/BD/100314/2014

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release