5XVD | pdb_00005xvd

[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an air-oxidized condition

PDB DOI: https://doi.org/10.2210/pdb5XVD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Citrobacter sp. S-77, Citrobacter sp. MGH106
Mutation(s): No

Deposited: 2017-06-27 Released: 2018-06-27
Deposition Author(s): Nishikawa, K., Matsuura, H., Muhd Noor, N.D., Tai, H., Hirota, S., Kim, J., Kang, J., Tateno, M., Yoon, K.S., Ogo, S., Shomura, Y., Higuchi, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.166 (Depositor), 0.166 (DCC)
R-Value Work:
0.121 (Depositor), 0.121 (DCC)
R-Value Observed:
0.123 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.

Noor, N.D.M., Matsuura, H., Nishikawa, K., Tai, H., Hirota, S., Kim, J., Kang, J., Tateno, M., Yoon, K.S., Ogo, S., Kubota, S., Shomura, Y., Higuchi, Y.

(2018) Chem Commun (Camb) 54: 12385-12388

PubMed: 30328414 Search on PubMed
DOI: https://doi.org/10.1039/c8cc06261g
Primary Citation Related Structures:
5XVB, 5XVC, 5XVD

PubMed Abstract:
Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

Organizational Affiliation

Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan. hig@sci.u-hyogo.ac.jp.

Macromolecule Content

Total Structure Weight: 197.22 kDa
Atom Count: 14,075
Modeled Residue Count: 1,640
Deposited Residue Count: 1,774
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[NiFe]-hydrogenase 2 large subunit	A [auth L], C [auth M]	552	Citrobacter sp. S-77	Mutation(s): 0 EC: 1.12.99.6
UniProt
Find proteins for A0A3B6UEQ1 (Citrobacter sp. S-77) Explore A0A3B6UEQ1 Go to UniProtKB: A0A3B6UEQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A3B6UEQ1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase-2 small chain	B [auth S], D [auth T]	335	Citrobacter sp. MGH106	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69741
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8JU Query on 8JU Download:Ideal Coordinates CCD File SDF format, chain M [auth S] SDF format, chain U [auth T] MOL2 format, chain M [auth S] MOL2 format, chain U [auth T] mmCIF format, chain M [auth S] mmCIF format, chain U [auth T]	M [auth S], U [auth T]	FE4-S4-O CLUSTER Fe₄ O S₄ RAQKYMZLKKCSFU-UHFFFAOYSA-N		Interactions Focus chain M [auth S] Focus chain U [auth T] Interactions & Density Focus chain M [auth S] Focus chain U [auth T]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain J [auth S] SDF format, chain L [auth S] SDF format, chain R [auth T] SDF format, chain T MOL2 format, chain J [auth S] MOL2 format, chain L [auth S] MOL2 format, chain R [auth T] MOL2 format, chain T mmCIF format, chain J [auth S] mmCIF format, chain L [auth S] mmCIF format, chain R [auth T] mmCIF format, chain T	J [auth S], L [auth S], R [auth T], T	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain J [auth S] Focus chain L [auth S] Focus chain R [auth T] Focus chain T Interactions & Density Focus chain J [auth S] Focus chain L [auth S] Focus chain R [auth T] Focus chain T
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain K [auth S] SDF format, chain S [auth T] MOL2 format, chain K [auth S] MOL2 format, chain S [auth T] mmCIF format, chain K [auth S] mmCIF format, chain S [auth T]	K [auth S], S [auth T]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain K [auth S] Focus chain S [auth T] Interactions & Density Focus chain K [auth S] Focus chain S [auth T]
NFV Query on NFV Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain P [auth M] MOL2 format, chain F [auth L] MOL2 format, chain P [auth M] mmCIF format, chain F [auth L] mmCIF format, chain P [auth M]	F [auth L], P [auth M]	NI-FE OXIDIZED ACTIVE CENTER C₃ Fe N₂ Ni O₂ MPQMGFDSXFFIQL-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain P [auth M] Interactions & Density Focus chain F [auth L] Focus chain P [auth M]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain N [auth S] SDF format, chain V [auth T] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain N [auth S] MOL2 format, chain V [auth T] mmCIF format, chain G [auth L] mmCIF format, chain H [auth L] mmCIF format, chain N [auth S] mmCIF format, chain V [auth T]	G [auth L], H [auth L], N [auth S], V [auth T]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth L] Focus chain H [auth L] Focus chain N [auth S] Focus chain V [auth T] Interactions & Density Focus chain G [auth L] Focus chain H [auth L] Focus chain N [auth S] Focus chain V [auth T]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth L] SDF format, chain O [auth M] MOL2 format, chain E [auth L] MOL2 format, chain O [auth M] mmCIF format, chain E [auth L] mmCIF format, chain O [auth M]	E [auth L], O [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth L] Focus chain O [auth M] Interactions & Density Focus chain E [auth L] Focus chain O [auth M]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A [auth L], C [auth M]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.166 (Depositor), 0.166 (DCC)
R-Value Work: 0.121 (Depositor), 0.121 (DCC)
R-Value Observed: 0.123 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.94	α = 90
b = 118.98	β = 100.57
c = 96.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-27
Type: Initial release
Version 1.1: 2019-07-10
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Derived calculations, Structure summary