6SZK

Hydrogenase-2 variant R479K - hydrogen reduced form treated with CO

• PDB DOI: https://doi.org/10.2210/pdb6SZK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12, Escherichia coli 908519
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-10-02 Released: 2020-10-14 
• Deposition Author(s): Carr, S.B., Beaton, S.E., Evans, R.M., Armstrong, F.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.141 
• R-Value Work: 0.121 

Starting Model: experimental

Literature

Hydrogen activation by NiFe-hydrogenases - consolidating the role of the pendant arginine.

Beaton, S.E., Evans, R.M., Kertess, L., Carr, S.B., Armstrong, F.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 192.62 kDa 
• Atom Count: 14,308 
• Modelled Residue Count: 1,638 
• Deposited Residue Count: 1,730 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-2 small chain	A [auth SSS], C [auth TTT]	298	Escherichia coli K-12	Mutation(s): 0  Gene Names: hybO, yghV, b2997, JW2965 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 LLL], D [auth MMM]	567	Escherichia coli 908519	Mutation(s): 1  Gene Names: HMPREF1604_02362

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	E [auth SSS], G [auth SSS], O [auth TTT], Q [auth TTT]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	F [auth SSS], P [auth TTT]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FCO (Subject of Investigation/LOI)	I [auth LLL], T [auth MMM]	CARBONMONOXIDE-(DICYANO) IRON C3 Fe N2 O VBQUCMTXYFMTTE-UHFFFAOYSA-N
GOL	H [auth SSS], Y [auth MMM]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)	J [auth LLL], U [auth MMM]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	M [auth LLL], W [auth MMM]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	N [auth LLL], X [auth MMM]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG	K [auth LLL], L [auth LLL], R [auth TTT], S [auth TTT], V [auth MMM]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.141 
• R-Value Work: 0.121 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.667	α = 90
b = 101.21	β = 90
c = 170.826	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Carr, S.B., Beaton, S.E., Evans, R.M., Armstrong, F.A.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary