9ER9 | pdb_00009er9

Hydrogenase-1 Ni-R state

PDB DOI: https://doi.org/10.2210/pdb9ER9/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: 1.40 ?
R-Value Free:
0.179 (Depositor), 0.182 (DCC)
R-Value Work:
0.164 (Depositor), 0.167 (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: 195.7 kDa
Atom Count: 15,022
Modelled Residue Count: 1,688
Deposited Residue Count: 1,722
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-1 small chain	A [auth S], C [auth T]	279	Escherichia coli	Mutation(s): 0 Gene Names: hyaA, b0972, JW0954 EC: 1.12.99.6
UniProt
Find proteins for P69739 (Escherichia coli (strain K12)) Explore P69739 Go to UniProtKB: P69739
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69739
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-1 large chain	B [auth L], D [auth M]	582	Escherichia coli	Mutation(s): 0 Gene Names: hyaB, b0973, JW0955 EC: 1.12.99.6
UniProt
Find proteins for P0ACD8 (Escherichia coli (strain K12)) Explore P0ACD8 Go to UniProtKB: P0ACD8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ACD8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H6N Query on A1H6N Download Ideal Coordinates CCD File SDF format, chain BA [auth M] SDF format, chain O [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain O [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain O [auth L]	BA [auth M], O [auth L]	2-[[2-[2-[2-[bis(2-hydroxy-2-oxoethyl)amino]phenoxy]ethoxy]phenyl]-(2-hydroxy-2-oxoethyl)amino]ethanoic acid C₂₂ H₂₄ N₂ O₁₀ FTEDXVNDVHYDQW-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain O [auth L] Interactions & Density Focus chain BA [auth M] Focus chain O [auth L]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth S] SDF format, chain R [auth T] MOL2 format, chain E [auth S] MOL2 format, chain R [auth T] mmCIF format, chain E [auth S] mmCIF format, chain R [auth T]	E [auth S], R [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain R [auth T] Interactions & Density Focus chain E [auth S] Focus chain R [auth T]
SF3 Query on SF3 Download Ideal Coordinates CCD File SDF format, chain G [auth S] SDF format, chain T MOL2 format, chain G [auth S] MOL2 format, chain T mmCIF format, chain G [auth S] mmCIF format, chain T	G [auth S], T	FE4-S3 CLUSTER Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N		Interactions Focus chain G [auth S] Focus chain T Interactions & Density Focus chain G [auth S] Focus chain T
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain F [auth S] SDF format, chain S [auth T] MOL2 format, chain F [auth S] MOL2 format, chain S [auth T] mmCIF format, chain F [auth S] mmCIF format, chain S [auth T]	F [auth S], S [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain S [auth T] Interactions & Density Focus chain F [auth S] Focus chain S [auth T]
EU Query on EU Download Ideal Coordinates CCD File SDF format, chain CA [auth M] SDF format, chain Q [auth L] MOL2 format, chain CA [auth M] MOL2 format, chain Q [auth L] mmCIF format, chain CA [auth M] mmCIF format, chain Q [auth L]	CA [auth M], Q [auth L]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain Q [auth L] Interactions & Density Focus chain CA [auth M] Focus chain Q [auth L]
FCO Query on FCO Download Ideal Coordinates CCD File SDF format, chain L SDF format, chain Y [auth M] MOL2 format, chain L MOL2 format, chain Y [auth M] mmCIF format, chain L mmCIF format, chain Y [auth M]	L, Y [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain L Focus chain Y [auth M] Interactions & Density Focus chain L Focus chain Y [auth M]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth L] MOL2 format, chain K [auth L] mmCIF format, chain K [auth L]	K [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth L] Interactions & Density Focus chain K [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth S] SDF format, chain J [auth S] SDF format, chain V [auth T] SDF format, chain W [auth T] MOL2 format, chain I [auth S] MOL2 format, chain J [auth S] MOL2 format, chain V [auth T] MOL2 format, chain W [auth T] mmCIF format, chain I [auth S] mmCIF format, chain J [auth S] mmCIF format, chain V [auth T] mmCIF format, chain W [auth T]	I [auth S], J [auth S], V [auth T], W [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth S] Focus chain J [auth S] Focus chain V [auth T] Focus chain W [auth T] Interactions & Density Focus chain I [auth S] Focus chain J [auth S] Focus chain V [auth T] Focus chain W [auth T]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain M [auth L] SDF format, chain Z [auth M] MOL2 format, chain M [auth L] MOL2 format, chain Z [auth M] mmCIF format, chain M [auth L] mmCIF format, chain Z [auth M]	M [auth L], Z [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Focus chain Z [auth M] Interactions & Density Focus chain M [auth L] Focus chain Z [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth S] SDF format, chain P [auth L] SDF format, chain U [auth T] SDF format, chain X [auth T] MOL2 format, chain H [auth S] MOL2 format, chain P [auth L] MOL2 format, chain U [auth T] MOL2 format, chain X [auth T] mmCIF format, chain H [auth S] mmCIF format, chain P [auth L] mmCIF format, chain U [auth T] mmCIF format, chain X [auth T]	H [auth S], P [auth L], U [auth T], X [auth T]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth S] Focus chain P [auth L] Focus chain U [auth T] Focus chain X [auth T] Interactions & Density Focus chain H [auth S] Focus chain P [auth L] Focus chain U [auth T] Focus chain X [auth T]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain N [auth L] MOL2 format, chain AA [auth M] MOL2 format, chain N [auth L] mmCIF format, chain AA [auth M] mmCIF format, chain N [auth L]	AA [auth M], N [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain N [auth L] Interactions & Density Focus chain AA [auth M] Focus chain N [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 ?
R-Value Free: 0.179 (Depositor), 0.182 (DCC)
R-Value Work: 0.164 (Depositor), 0.167 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 93.569	α = 90
b = 97.065	β = 90
c = 182.877	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