6G94

Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b

PDB DOI: https://doi.org/10.2210/pdb6G94/pdb

Classification: OXIDOREDUCTASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes OPMPDBTM

Deposited: 2018-04-10 Released: 2018-06-13
Deposition Author(s): Volbeda, A., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.222
R-Value Observed: 0.223

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster.

Volbeda, A., Mouesca, J.M., Darnault, C., Roessler, M.M., Parkin, A., Armstrong, F.A., Fontecilla-Camps, J.C.

(2018) Chem Commun (Camb) 54: 7175-7178

PubMed: 29888350 Search on PubMed
DOI: https://doi.org/10.1039/c8cc02896f
Primary Citation of Related Structures:
6G94

PubMed Abstract:
The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.

Organizational Affiliation

Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France. anne.volbeda@ibs.fr.

Macromolecule Content

Total Structure Weight: 467.58 kDa
Atom Count: 30,463
Modelled Residue Count: 3,834
Deposited Residue Count: 4,138
Unique protein chains: 3

Macromolecules

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(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], E [auth Q], G [auth R]	335	Escherichia coli K-12	Mutation(s): 0 Gene Names: hyaA, b0972, JW0954 EC: 1.12.99.6 Membrane Entity: Yes
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

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(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], F [auth J], H [auth K]	582	Escherichia coli K-12	Mutation(s): 0 Gene Names: hyaB, b0973, JW0955 EC: 1.12.99.6 Membrane Entity: Yes
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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit	I [auth A], J [auth B]	235	Escherichia coli K-12	Mutation(s): 0 Gene Names: hyaC, b0974, JW0956 Membrane Entity: Yes
UniProt
Find proteins for P0AAM1 (Escherichia coli (strain K12)) Explore P0AAM1 Go to UniProtKB: P0AAM1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AAM1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain MA [auth A] SDF format, chain NA [auth B] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth B] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth B]	MA [auth A], NA [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain MA [auth A] Focus chain NA [auth B] Interactions & Density Focus chain MA [auth A] Focus chain NA [auth B]
ER2 Query on ER2 Download Ideal Coordinates CCD File SDF format, chain AA [auth Q] SDF format, chain HA [auth R] SDF format, chain M [auth S] SDF format, chain T MOL2 format, chain AA [auth Q] MOL2 format, chain HA [auth R] MOL2 format, chain M [auth S] MOL2 format, chain T mmCIF format, chain AA [auth Q] mmCIF format, chain HA [auth R] mmCIF format, chain M [auth S] mmCIF format, chain T	AA [auth Q], HA [auth R], M [auth S], T	Fe4S4 Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth Q] Focus chain HA [auth R] Focus chain M [auth S] Focus chain T Interactions & Density Focus chain AA [auth Q] Focus chain HA [auth R] Focus chain M [auth S] Focus chain T
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain FA [auth R] SDF format, chain K [auth S] SDF format, chain R [auth T] SDF format, chain Y [auth Q] MOL2 format, chain FA [auth R] MOL2 format, chain K [auth S] MOL2 format, chain R [auth T] MOL2 format, chain Y [auth Q] mmCIF format, chain FA [auth R] mmCIF format, chain K [auth S] mmCIF format, chain R [auth T] mmCIF format, chain Y [auth Q]	FA [auth R], K [auth S], R [auth T], Y [auth Q]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain FA [auth R] Focus chain K [auth S] Focus chain R [auth T] Focus chain Y [auth Q] Interactions & Density Focus chain FA [auth R] Focus chain K [auth S] Focus chain R [auth T] Focus chain Y [auth Q]
F3S Query on F3S Download Ideal Coordinates CCD File SDF format, chain GA [auth R] SDF format, chain L [auth S] SDF format, chain S [auth T] SDF format, chain Z [auth Q] MOL2 format, chain GA [auth R] MOL2 format, chain L [auth S] MOL2 format, chain S [auth T] MOL2 format, chain Z [auth Q] mmCIF format, chain GA [auth R] mmCIF format, chain L [auth S] mmCIF format, chain S [auth T] mmCIF format, chain Z [auth Q]	GA [auth R], L [auth S], S [auth T], Z [auth Q]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain GA [auth R] Focus chain L [auth S] Focus chain S [auth T] Focus chain Z [auth Q] Interactions & Density Focus chain GA [auth R] Focus chain L [auth S] Focus chain S [auth T] Focus chain Z [auth Q]
FCO Query on FCO Download Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain IA [auth K] SDF format, chain N [auth L] SDF format, chain U [auth M] MOL2 format, chain BA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain N [auth L] MOL2 format, chain U [auth M] mmCIF format, chain BA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain N [auth L] mmCIF format, chain U [auth M]	BA [auth J], IA [auth K], N [auth L], U [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain BA [auth J] Focus chain IA [auth K] Focus chain N [auth L] Focus chain U [auth M] Interactions & Density Focus chain BA [auth J] Focus chain IA [auth K] Focus chain N [auth L] Focus chain U [auth M]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain JA [auth K] SDF format, chain O [auth L] SDF format, chain V [auth M] MOL2 format, chain CA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain O [auth L] MOL2 format, chain V [auth M] mmCIF format, chain CA [auth J] mmCIF format, chain JA [auth K] mmCIF format, chain O [auth L] mmCIF format, chain V [auth M]	CA [auth J], JA [auth K], O [auth L], V [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain JA [auth K] Focus chain O [auth L] Focus chain V [auth M] Interactions & Density Focus chain CA [auth J] Focus chain JA [auth K] Focus chain O [auth L] Focus chain V [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain EA [auth J] SDF format, chain LA [auth K] SDF format, chain Q [auth L] SDF format, chain X [auth M] MOL2 format, chain EA [auth J] MOL2 format, chain LA [auth K] MOL2 format, chain Q [auth L] MOL2 format, chain X [auth M] mmCIF format, chain EA [auth J] mmCIF format, chain LA [auth K] mmCIF format, chain Q [auth L] mmCIF format, chain X [auth M]	EA [auth J], LA [auth K], Q [auth L], X [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth J] Focus chain LA [auth K] Focus chain Q [auth L] Focus chain X [auth M] Interactions & Density Focus chain EA [auth J] Focus chain LA [auth K] Focus chain Q [auth L] Focus chain X [auth M]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain DA [auth J] SDF format, chain KA [auth K] SDF format, chain P [auth L] SDF format, chain W [auth M] MOL2 format, chain DA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain P [auth L] MOL2 format, chain W [auth M] mmCIF format, chain DA [auth J] mmCIF format, chain KA [auth K] mmCIF format, chain P [auth L] mmCIF format, chain W [auth M]	DA [auth J], KA [auth K], P [auth L], W [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth J] Focus chain KA [auth K] Focus chain P [auth L] Focus chain W [auth M] Interactions & Density Focus chain DA [auth J] Focus chain KA [auth K] Focus chain P [auth L] Focus chain W [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.222
R-Value Observed: 0.223
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.41	α = 90
b = 165.03	β = 90
c = 206.22	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Volbeda, A.

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2018-06-20
Changes: Data collection, Database references
Version 1.2: 2018-07-04
Changes: Data collection, Database references
Version 1.3: 2019-08-21
Changes: Data collection, Database references
Version 1.4: 2020-02-05
Changes: Database references, Source and taxonomy
Version 1.5: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description