5XVB

[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition

• PDB DOI: https://doi.org/10.2210/pdb5XVB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Citrobacter sp. S-77
• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

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 
• DOI: https://doi.org/10.1039/c8cc06261g
• Primary Citation of 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.

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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. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 199.49 kDa 
• Atom Count: 13,266 
• Modelled Residue Count: 1,638 
• Deposited Residue Count: 1,804 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[NiFe]-hydrogenase 2 large subunit	A [auth L], C [auth M]	567	Citrobacter sp. S-77	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEP7 (Citrobacter sp. S-77) Explore A0A3B6UEP7  Go to UniProtKB:  A0A3B6UEP7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
[NiFe]-hydrogenase 2 small subunit	B [auth S], D [auth T]	335	Citrobacter sp. S-77	Mutation(s): 0
UniProt
Find proteins for A0A3B6UEQ0 (Citrobacter sp. S-77) Explore A0A3B6UEQ0  Go to UniProtKB:  A0A3B6UEQ0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	I [auth S], K [auth S], O [auth T], Q [auth T]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	J [auth S], P [auth T]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFU	F [auth L], M	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni) C3 H Fe N2 Ni O QCZROEOIPZWDEO-UHFFFAOYSA-N
GOL	G [auth L], H [auth L], N [auth M], R [auth T]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth L], L [auth M]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.73	α = 90
b = 121.61	β = 102.65
c = 98.88	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• 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: 2024-03-27
  Changes: Data collection, Database references, Derived calculations