9ERC | pdb_00009erc

Hydrogenase-2 Ni-Li state

PDB DOI: https://doi.org/10.2210/pdb9ERC/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): Wong, K.L., Carr, S.B., Ash, P.A., Vincent, K.A.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.193 (Depositor), 0.198 (DCC)
R-Value Work:
0.174 (Depositor), 0.181 (DCC)

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: 193.82 kDa
Atom Count: 14,333
Modeled Residue Count: 1,636
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain Y [auth T] SDF format, chain W [auth T] SDF format, chain G [auth S] SDF format, chain E [auth S] MOL2 format, chain Y [auth T] MOL2 format, chain W [auth T] MOL2 format, chain G [auth S] MOL2 format, chain E [auth S] mmCIF format, chain Y [auth T] mmCIF format, chain W [auth T] mmCIF format, chain G [auth S] mmCIF format, chain E [auth S]	E [auth S], G [auth S], W [auth T], Y [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain G [auth S] Focus chain W [auth T] Focus chain Y [auth T] Interactions & Density Focus chain E [auth S] Focus chain G [auth S] Focus chain W [auth T] Focus chain Y [auth T]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain X [auth T] SDF format, chain F [auth S] MOL2 format, chain X [auth T] MOL2 format, chain F [auth S] mmCIF format, chain X [auth T] mmCIF format, chain F [auth S]	F [auth S], X [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain X [auth T] Interactions & Density Focus chain F [auth S] Focus chain X [auth T]
FCO (Subject of Investigation/LOI) Query on FCO Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain M [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain M [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain M [auth L]	BA [auth M], M [auth L]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain M [auth L] Interactions & Density Focus chain BA [auth M] Focus chain M [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth T] SDF format, chain V [auth T] SDF format, chain R [auth L] SDF format, chain Q [auth L] SDF format, chain P [auth L] SDF format, chain L SDF format, chain J [auth S] SDF format, chain IA [auth M] SDF format, chain I [auth S] SDF format, chain HA [auth M] SDF format, chain H [auth S] SDF format, chain GA [auth M] SDF format, chain FA [auth M] SDF format, chain EA [auth M] SDF format, chain AA [auth M] MOL2 format, chain Z [auth T] MOL2 format, chain V [auth T] MOL2 format, chain R [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain P [auth L] MOL2 format, chain L MOL2 format, chain J [auth S] MOL2 format, chain IA [auth M] MOL2 format, chain I [auth S] MOL2 format, chain HA [auth M] MOL2 format, chain H [auth S] MOL2 format, chain GA [auth M] MOL2 format, chain FA [auth M] MOL2 format, chain EA [auth M] MOL2 format, chain AA [auth M] mmCIF format, chain Z [auth T] mmCIF format, chain V [auth T] mmCIF format, chain R [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain P [auth L] mmCIF format, chain L mmCIF format, chain J [auth S] mmCIF format, chain IA [auth M] mmCIF format, chain I [auth S] mmCIF format, chain HA [auth M] mmCIF format, chain H [auth S] mmCIF format, chain GA [auth M] mmCIF format, chain FA [auth M] mmCIF format, chain EA [auth M] mmCIF format, chain AA [auth M]	AA [auth M] EA [auth M] FA [auth M] GA [auth M] H [auth S] AA [auth M], EA [auth M], FA [auth M], GA [auth M], H [auth S], HA [auth M], I [auth S], IA [auth M], J [auth S], L, P [auth L], Q [auth L], R [auth L], V [auth T], Z [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain EA [auth M] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain H [auth S] Focus chain HA [auth M] Focus chain I [auth S] Focus chain IA [auth M] Focus chain J [auth S] Focus chain L Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain V [auth T] Focus chain Z [auth T] Interactions & Density Focus chain AA [auth M] Focus chain EA [auth M] Focus chain FA [auth M] Focus chain GA [auth M] Focus chain H [auth S] Focus chain HA [auth M] Focus chain I [auth S] Focus chain IA [auth M] Focus chain J [auth S] Focus chain L Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain V [auth T] Focus chain Z [auth T]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain N [auth L] SDF format, chain CA [auth M] MOL2 format, chain N [auth L] MOL2 format, chain CA [auth M] mmCIF format, chain N [auth L] mmCIF format, chain CA [auth M]	CA [auth M], N [auth L]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain N [auth L] Interactions & Density Focus chain CA [auth M] Focus chain N [auth L]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain U [auth L] SDF format, chain T [auth L] SDF format, chain S [auth L] SDF format, chain O [auth L] SDF format, chain KA [auth M] SDF format, chain K [auth S] SDF format, chain JA [auth M] SDF format, chain DA [auth M] MOL2 format, chain U [auth L] MOL2 format, chain T [auth L] MOL2 format, chain S [auth L] MOL2 format, chain O [auth L] MOL2 format, chain KA [auth M] MOL2 format, chain K [auth S] MOL2 format, chain JA [auth M] MOL2 format, chain DA [auth M] mmCIF format, chain U [auth L] mmCIF format, chain T [auth L] mmCIF format, chain S [auth L] mmCIF format, chain O [auth L] mmCIF format, chain KA [auth M] mmCIF format, chain K [auth S] mmCIF format, chain JA [auth M] mmCIF format, chain DA [auth M]	DA [auth M] JA [auth M] K [auth S] KA [auth M] O [auth L] DA [auth M], JA [auth M], K [auth S], KA [auth M], O [auth L], S [auth L], T [auth L], U [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth M] Focus chain JA [auth M] Focus chain K [auth S] Focus chain KA [auth M] Focus chain O [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L] Interactions & Density Focus chain DA [auth M] Focus chain JA [auth M] Focus chain K [auth S] Focus chain KA [auth M] Focus chain O [auth L] Focus chain S [auth L] Focus chain T [auth L] Focus chain U [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.193 (Depositor), 0.198 (DCC)
R-Value Work: 0.174 (Depositor), 0.181 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.877	α = 90
b = 99.974	β = 90
c = 168.071	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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