6G7M | pdb_00006g7m

Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydrogenase-2

• PDB DOI: https://doi.org/10.2210/pdb6G7M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2018-04-06 Released: 2019-04-03 
• Deposition Author(s): Carr, S.B., Armstrong, F.A., Zhang, L., Beaton, S.E.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.190 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Direct visible light activation of a surface cysteine-engineered [NiFe]-hydrogenase by silver nanoclusters

Zhang, L., Beaton, S.E., Carr, S.B., Armstrong, F.A.

(2019) Energy Environ Sci 

• DOI: https://doi.org/10.1039/C8EE02361A

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 193.47 kDa 
• Atom Count: 13,667 
• Modeled Residue Count: 1,638 
• Deposited Residue Count: 1,742 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-2 small chain	A [auth S], C [auth T]	304	Escherichia coli K-12	Mutation(s): 0  EC: 1.12.99.6
UniProt
Find proteins for P69741 (Escherichia coli (strain K12)) Explore P69741  Go to UniProtKB:  P69741

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-2 large chain	B [auth L], D [auth M]	567	Escherichia coli K-12	Mutation(s): 3  EC: 1.12.99.6
UniProt
Find proteins for P0ACE0 (Escherichia coli (strain K12)) Explore P0ACE0  Go to UniProtKB:  P0ACE0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	E [auth S], G [auth S], L [auth T], N [auth T]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	F [auth S], M [auth T]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FCO	H [auth L], O [auth M]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI	I [auth L], P [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
MG	J [auth L], K [auth L], Q [auth M], R [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.190 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.237	α = 90
b = 100.986	β = 90
c = 169.425	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Carr, S.B., Armstrong, F.A., Zhang, L., Beaton, S.E.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N006321/1

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary