6SYX

Hydrogenase-2 variant R479K - reduced sample exposed to pure oxygen

PDB DOI: https://doi.org/10.2210/pdb6SYX/pdb

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

Deposited: 2019-10-01 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: 1.30 Å
R-Value Free: 0.163
R-Value Work: 0.147

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 193.07 kDa
Atom Count: 14,669
Modelled Residue Count: 1,638
Deposited Residue Count: 1,730
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69741
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth SSS] SDF format, chain G [auth SSS] SDF format, chain S [auth TTT] SDF format, chain U [auth TTT] MOL2 format, chain E [auth SSS] MOL2 format, chain G [auth SSS] MOL2 format, chain S [auth TTT] MOL2 format, chain U [auth TTT]	E [auth SSS], G [auth SSS], S [auth TTT], U [auth TTT]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth SSS] Focus chain G [auth SSS] Focus chain S [auth TTT] Focus chain U [auth TTT] Interactions & Density Focus chain E [auth SSS] Focus chain G [auth SSS] Focus chain S [auth TTT] Focus chain U [auth TTT]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain F [auth SSS] SDF format, chain T [auth TTT] MOL2 format, chain F [auth SSS] MOL2 format, chain T [auth TTT]	F [auth SSS], T [auth TTT]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth SSS] Focus chain T [auth TTT] Interactions & Density Focus chain F [auth SSS] Focus chain T [auth TTT]
FCO (Subject of Investigation/LOI) Query on FCO Download Ideal Coordinates CCD File SDF format, chain K [auth LLL] SDF format, chain X [auth MMM] MOL2 format, chain K [auth LLL] MOL2 format, chain X [auth MMM]	K [auth LLL], X [auth MMM]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain K [auth LLL] Focus chain X [auth MMM] Interactions & Density Focus chain K [auth LLL] Focus chain X [auth MMM]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth MMM] SDF format, chain H [auth SSS] SDF format, chain I [auth SSS] SDF format, chain J [auth LLL] SDF format, chain N [auth LLL] SDF format, chain R [auth TTT] SDF format, chain W [auth MMM] MOL2 format, chain AA [auth MMM] MOL2 format, chain H [auth SSS] MOL2 format, chain I [auth SSS] MOL2 format, chain J [auth LLL] MOL2 format, chain N [auth LLL] MOL2 format, chain R [auth TTT] MOL2 format, chain W [auth MMM]	AA [auth MMM] H [auth SSS] I [auth SSS] J [auth LLL] N [auth LLL] AA [auth MMM], H [auth SSS], I [auth SSS], J [auth LLL], N [auth LLL], R [auth TTT], W [auth MMM]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth MMM] Focus chain H [auth SSS] Focus chain I [auth SSS] Focus chain J [auth LLL] Focus chain N [auth LLL] Focus chain R [auth TTT] Focus chain W [auth MMM] Interactions & Density Focus chain AA [auth MMM] Focus chain H [auth SSS] Focus chain I [auth SSS] Focus chain J [auth LLL] Focus chain N [auth LLL] Focus chain R [auth TTT] Focus chain W [auth MMM]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain L [auth LLL] SDF format, chain Y [auth MMM] MOL2 format, chain L [auth LLL] MOL2 format, chain Y [auth MMM]	L [auth LLL], Y [auth MMM]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain L [auth LLL] Focus chain Y [auth MMM] Interactions & Density Focus chain L [auth LLL] Focus chain Y [auth MMM]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth MMM] SDF format, chain P [auth LLL] MOL2 format, chain BA [auth MMM] MOL2 format, chain P [auth LLL]	BA [auth MMM], P [auth LLL]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth MMM] Focus chain P [auth LLL] Interactions & Density Focus chain BA [auth MMM] Focus chain P [auth LLL]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain CA [auth MMM] SDF format, chain Q [auth LLL] MOL2 format, chain CA [auth MMM] MOL2 format, chain Q [auth LLL]	CA [auth MMM], Q [auth LLL]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain CA [auth MMM] Focus chain Q [auth LLL] Interactions & Density Focus chain CA [auth MMM] Focus chain Q [auth LLL]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth LLL] SDF format, chain O [auth LLL] SDF format, chain V [auth TTT] SDF format, chain Z [auth MMM] MOL2 format, chain M [auth LLL] MOL2 format, chain O [auth LLL] MOL2 format, chain V [auth TTT] MOL2 format, chain Z [auth MMM]	M [auth LLL], O [auth LLL], V [auth TTT], Z [auth MMM]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth LLL] Focus chain O [auth LLL] Focus chain V [auth TTT] Focus chain Z [auth MMM] Interactions & Density Focus chain M [auth LLL] Focus chain O [auth LLL] Focus chain V [auth TTT] Focus chain Z [auth MMM]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.163
R-Value Work: 0.147
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.729	α = 90
b = 101.332	β = 90
c = 170.681	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-10-14

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-10-14
Type: Initial release
Version 2.0: 2024-01-24
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description