9ERB | pdb_00009erb

Hydrogenase-2 Ni-B state

PDB DOI: https://doi.org/10.2210/pdb9ERB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-22 Released: 2025-04-02
Deposition Author(s): Carr, S.B., Li, W., Wong, K.l., Ash, P.A., Vincent, K.A.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 ?
R-Value Free:
0.161 (Depositor), 0.162 (DCC)
R-Value Work:
0.145 (Depositor), 0.147 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Glutamate flick enables proton tunnelling during fast redox biocatalysis

Carr, S.B., Li, W., Wong, K.l., Evans, R.M., Kendall-Price, S.E.T., Ash, P.A., Vincent, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 192.66 kDa
Atom Count: 14,466
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 S], C [auth T]	298	Escherichia coli	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 L], D [auth M]	567	Escherichia coli	Mutation(s): 0 Gene Names: hybC, b2994, JW2962 EC: 1.12.99.6
UniProt
Find proteins for P0ACE0 (Escherichia coli (strain K12)) Explore P0ACE0 Go to UniProtKB: P0ACE0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ACE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 S] SDF format, chain G [auth S] SDF format, chain N [auth T] SDF format, chain P [auth T] MOL2 format, chain E [auth S] MOL2 format, chain G [auth S] MOL2 format, chain N [auth T] MOL2 format, chain P [auth T] mmCIF format, chain E [auth S] mmCIF format, chain G [auth S] mmCIF format, chain N [auth T] mmCIF format, chain P [auth T]	E [auth S], G [auth S], N [auth T], P [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain G [auth S] Focus chain N [auth T] Focus chain P [auth T] Interactions & Density Focus chain E [auth S] Focus chain G [auth S] Focus chain N [auth T] Focus chain P [auth T]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain F [auth S] SDF format, chain O [auth T] MOL2 format, chain F [auth S] MOL2 format, chain O [auth T] mmCIF format, chain F [auth S] mmCIF format, chain O [auth T]	F [auth S], O [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain O [auth T] Interactions & Density Focus chain F [auth S] Focus chain O [auth T]
FCO (Subject of Investigation/LOI) Query on FCO Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain R [auth M] MOL2 format, chain I [auth L] MOL2 format, chain R [auth M] mmCIF format, chain I [auth L] mmCIF format, chain R [auth M]	I [auth L], R [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain R [auth M] Interactions & Density Focus chain I [auth L] Focus chain R [auth M]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth S] SDF format, chain Q [auth T] SDF format, chain V [auth M] MOL2 format, chain H [auth S] MOL2 format, chain Q [auth T] MOL2 format, chain V [auth M] mmCIF format, chain H [auth S] mmCIF format, chain Q [auth T] mmCIF format, chain V [auth M]	H [auth S], Q [auth T], V [auth M]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth S] Focus chain Q [auth T] Focus chain V [auth M] Interactions & Density Focus chain H [auth S] Focus chain Q [auth T] Focus chain V [auth M]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain S [auth M] MOL2 format, chain J [auth L] MOL2 format, chain S [auth M] mmCIF format, chain J [auth L] mmCIF format, chain S [auth M]	J [auth L], S [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth L] Focus chain S [auth M] Interactions & Density Focus chain J [auth L] Focus chain S [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth L] SDF format, chain L SDF format, chain T [auth M] SDF format, chain U [auth M] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain T [auth M] MOL2 format, chain U [auth M] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain T [auth M] mmCIF format, chain U [auth M]	K [auth L], L, T [auth M], U [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth L] Focus chain L Focus chain T [auth M] Focus chain U [auth M] Interactions & Density Focus chain K [auth L] Focus chain L Focus chain T [auth M] Focus chain U [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 ?
R-Value Free: 0.161 (Depositor), 0.162 (DCC)
R-Value Work: 0.145 (Depositor), 0.147 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 99.737	α = 90
b = 100.188	β = 90
c = 168.477	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R018413/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X002624/1