6G7M | pdb_00006g7m

Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydrogenase-2

PDB DOI: https://doi.org/10.2210/pdb6G7M/pdb

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

Deposited: 2018-04-06 Released: 2019-04-03
Deposition Author(s): Carr, S.B., Armstrong, F.A., Zhang, L., Beaton, S.E.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.190 (Depositor), 0.200 (DCC)
R-Value Work:
0.157 (Depositor), 0.170 (DCC)
R-Value Observed:
0.159 (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

Direct visible light activation of a surface cysteine-engineered [NiFe]-hydrogenase by silver nanoclusters

Zhang, L., Beaton, S.E., Carr, S.B., Armstrong, F.A.

(2019) Energy Environ Sci

DOI: https://doi.org/10.1039/C8EE02361A

Macromolecule Content

Total Structure Weight: 193.47 kDa
Atom Count: 13,667
Modeled Residue Count: 1,638
Deposited Residue Count: 1,742
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]	304	Escherichia coli K-12	Mutation(s): 0 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 K-12	Mutation(s): 3 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 5 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 L [auth T] SDF format, chain N [auth T] MOL2 format, chain E [auth S] MOL2 format, chain G [auth S] MOL2 format, chain L [auth T] MOL2 format, chain N [auth T] mmCIF format, chain E [auth S] mmCIF format, chain G [auth S] mmCIF format, chain L [auth T] mmCIF format, chain N [auth T]	E [auth S], G [auth S], L [auth T], N [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain G [auth S] Focus chain L [auth T] Focus chain N [auth T] Interactions & Density Focus chain E [auth S] Focus chain G [auth S] Focus chain L [auth T] Focus chain N [auth T]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain F [auth S] SDF format, chain M [auth T] MOL2 format, chain F [auth S] MOL2 format, chain M [auth T] mmCIF format, chain F [auth S] mmCIF format, chain M [auth T]	F [auth S], M [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth S] Focus chain M [auth T] Interactions & Density Focus chain F [auth S] Focus chain M [auth T]
FCO Query on FCO Download Ideal Coordinates CCD File SDF format, chain H [auth L] SDF format, chain O [auth M] MOL2 format, chain H [auth L] MOL2 format, chain O [auth M] mmCIF format, chain H [auth L] mmCIF format, chain O [auth M]	H [auth L], O [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain O [auth M] Interactions & Density Focus chain H [auth L] Focus chain O [auth M]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain P [auth M] MOL2 format, chain I [auth L] MOL2 format, chain P [auth M] mmCIF format, chain I [auth L] mmCIF format, chain P [auth M]	I [auth L], P [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain I [auth L] Focus chain P [auth M] Interactions & Density Focus chain I [auth L] Focus chain P [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 Q [auth M] SDF format, chain R [auth M] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M]	J [auth L], K [auth L], Q [auth M], R [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth L] Focus chain K [auth L] Focus chain Q [auth M] Focus chain R [auth M] Interactions & Density Focus chain J [auth L] Focus chain K [auth L] Focus chain Q [auth M] Focus chain R [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.190 (Depositor), 0.200 (DCC)
R-Value Work: 0.157 (Depositor), 0.170 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.237	α = 90
b = 100.986	β = 90
c = 169.425	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/N006321/1

Revision History (Full details and data files)

Version 1.0: 2019-04-03
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary