6EHQ

E. coli Hydrogenase-2 (as isolated form).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The structure of hydrogenase-2 fromEscherichia coli: implications for H2-driven proton pumping.

Beaton, S.E.Evans, R.M.Finney, A.J.Lamont, C.M.Armstrong, F.A.Sargent, F.Carr, S.B.

(2018) Biochem. J. 475: 1353-1370


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-2 small chain
S, T
300Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hybO (yghV)
EC: 1.12.99.6
Find proteins for P69741 (Escherichia coli (strain K12))
Go to UniProtKB:  P69741
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-2 large chain
L, M
552Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hybC
EC: 1.12.99.6
Find proteins for P0ACE0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACE0
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

Download SDF File 
Download CCD File 
L, M
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
L, M
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.064α = 90.00
b = 100.090β = 90.00
c = 168.135γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N006321/1

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references
  • Version 2.0: 2018-07-11
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary