6G7R

Structure of fully reduced variant E28Q of E. coli hydrogenase-1 at pH 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.111 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase.

Evans, R.M.Ash, P.A.Beaton, S.E.Brooke, E.J.Vincent, K.A.Carr, S.B.Armstrong, F.A.

(2018) J. Am. Chem. Soc. 140: 10208-10220


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 small chain
S, T
335Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hyaA
EC: 1.12.99.6
Find proteins for P69739 (Escherichia coli (strain K12))
Go to UniProtKB:  P69739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hydrogenase-1 large chain
L, M
582Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hyaB
EC: 1.12.99.6
Find proteins for P0ACD8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACD8
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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Download CCD File 
S, T
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
S, T
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
L, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EJ2
Query on EJ2

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Download CCD File 
L, M
NI-FE REDUCED ACTIVE CENTER
C3 H Fe N2 Ni O
JIXQCBCEPWXSQU-UHFFFAOYSA-O
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
S, T
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
SF3
Query on SF3

Download SDF File 
Download CCD File 
S, T
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.133 
  • R-Value Work: 0.111 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 94.068α = 90.00
b = 97.814β = 90.00
c = 183.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

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: 2019-02-27
    Type: Initial release