7NEM | pdb_00007nem

Hydrogenase-2 variant R479K - anaerobically oxidised form

PDB DOI: https://doi.org/10.2210/pdb7NEM/pdb

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

Deposited: 2021-02-04 Released: 2022-03-02
Deposition Author(s): Carr, S.B.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.167 (Depositor), 0.174 (DCC)
R-Value Work:
0.150 (Depositor), 0.160 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A comprehensive structural and kinetic investigation of the role of the active-site argininein bidirectional hydrogen activation by the [NiFe]-hydrogenase "Hyd-2) from Escherichia coli

Evans, R.M., Beaton, S.E., Kertiss, L., Myers, W.K., Carr, S.B., Armstrong, F.A.

To be published.

Macromolecule Content

Total Structure Weight: 192.39 kDa
Atom Count: 14,108
Modeled Residue Count: 1,638
Deposited Residue Count: 1,730
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 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 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69741
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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 K-12	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 M [auth T] SDF format, chain O [auth T] SDF format, chain G [auth S] MOL2 format, chain E [auth S] MOL2 format, chain M [auth T] MOL2 format, chain O [auth T] MOL2 format, chain G [auth S] mmCIF format, chain E [auth S] mmCIF format, chain M [auth T] mmCIF format, chain O [auth T] mmCIF format, chain G [auth S]	E [auth S], G [auth S], M [auth T], O [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain G [auth S] Focus chain M [auth T] Focus chain O [auth T] Interactions & Density Focus chain E [auth S] Focus chain G [auth S] Focus chain M [auth T] Focus chain O [auth T]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain F [auth S] SDF format, chain N [auth T] MOL2 format, chain F [auth S] MOL2 format, chain N [auth T] mmCIF format, chain F [auth S] mmCIF format, chain N [auth T]	F [auth S], N [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain N [auth T] Interactions & Density Focus chain F [auth S] Focus chain N [auth T]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain P [auth M] MOL2 format, chain H [auth L] MOL2 format, chain P [auth M] mmCIF format, chain H [auth L] mmCIF format, chain P [auth M]	H [auth L], P [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain P [auth M] Interactions & Density Focus chain H [auth L] Focus chain P [auth M]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain Q [auth M] MOL2 format, chain I [auth L] MOL2 format, chain Q [auth M] mmCIF format, chain I [auth L] mmCIF format, chain Q [auth M]	I [auth L], Q [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain Q [auth M] Interactions & Density Focus chain I [auth L] Focus chain Q [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain T [auth M] MOL2 format, chain T [auth M] mmCIF format, chain T [auth M]	T [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth M] Interactions & Density Focus chain T [auth M]
OXY (Subject of Investigation/LOI) Query on OXY Download:Ideal Coordinates CCD File SDF format, chain L SDF format, chain U [auth M] MOL2 format, chain L MOL2 format, chain U [auth M] mmCIF format, chain L mmCIF format, chain U [auth M]	L, U [auth M]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain L Focus chain U [auth M] Interactions & Density Focus chain L Focus chain U [auth M]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain R [auth M] SDF format, chain S [auth M] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M]	J [auth L], K [auth L], R [auth M], S [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth L] Focus chain K [auth L] Focus chain R [auth M] Focus chain S [auth M] Interactions & Density Focus chain J [auth L] Focus chain K [auth L] Focus chain R [auth M] Focus chain S [auth M]