5XFA | pdb_00005xfa

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the H2-reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis of the redox switches in the NAD(+)-reducing soluble [NiFe]-hydrogenase

Shomura, Y.Taketa, M.Nakashima, H.Tai, H.Nakagawa, H.Ikeda, Y.Ishii, M.Igarashi, Y.Nishihara, H.Yoon, K.S.Ogo, S.Hirota, S.Higuchi, Y.

(2017) Science 357: 928-932

  • DOI: https://doi.org/10.1126/science.aan4497
  • Primary Citation Related Structures: 
    5XF9, 5XFA

  • PubMed Abstract: 

    NAD + (oxidized form of NAD:nicotinamide adenine dinucleotide)-reducing soluble [NiFe]-hydrogenase (SH) is phylogenetically related to NADH (reduced form of NAD + ):quinone oxidoreductase (complex I), but the geometrical arrangements of the subunits and Fe-S clusters are unclear. Here, we describe the crystal structures of SH in the oxidized and reduced states. The cluster arrangement is similar to that of complex I, but the subunits orientation is not, which supports the hypothesis that subunits evolved as prebuilt modules. The oxidized active site includes a six-coordinate Ni, which is unprecedented for hydrogenases, whose coordination geometry would prevent O 2 from approaching. In the reduced state showing the normal active site structure without a physiological electron acceptor, the flavin mononucleotide cofactor is dissociated, which may be caused by the oxidation state change of nearby Fe-S clusters and may suppress production of reactive oxygen species.


  • Organizational Affiliation
    • Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki 316-8511, Japan. hig@sci.u-hyogo.ac.jp yasuhito.shomura.s@vc.ibaraki.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 330.31 kDa 
  • Atom Count: 22,444 
  • Modeled Residue Count: 2,879 
  • Deposited Residue Count: 2,980 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase
A, E
591Hydrogenophilus thermoluteolusMutation(s): 0 
UniProt
Find proteins for A0A077L6X8 (Hydrogenophilus thermoluteolus)
Explore A0A077L6X8 
Go to UniProtKB:  A0A077L6X8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077L6X8
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase
B, F
242Hydrogenophilus thermoluteolusMutation(s): 0 
UniProt
Find proteins for A0A077L885 (Hydrogenophilus thermoluteolus)
Explore A0A077L885 
Go to UniProtKB:  A0A077L885
Entity Groups
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UniProt GroupA0A077L885
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase
C, G
189Hydrogenophilus thermoluteolusMutation(s): 0 
UniProt
Find proteins for A0A077L7R5 (Hydrogenophilus thermoluteolus)
Explore A0A077L7R5 
Go to UniProtKB:  A0A077L7R5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077L7R5
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-reducing hydrogenase
D, H
468Hydrogenophilus thermoluteolusMutation(s): 0 
UniProt
Find proteins for A0A077LAI5 (Hydrogenophilus thermoluteolus)
Explore A0A077LAI5 
Go to UniProtKB:  A0A077LAI5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077LAI5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4

Query on SF4



Download:Ideal Coordinates CCD File
I [auth A]
J [auth B]
K [auth B]
M [auth C]
Q [auth E]
I [auth A],
J [auth B],
K [auth B],
M [auth C],
Q [auth E],
R [auth F],
S [auth F],
U [auth G]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
L [auth B],
T [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
FCO

Query on FCO



Download:Ideal Coordinates CCD File
N [auth D],
V [auth H]
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
NI

Query on NI



Download:Ideal Coordinates CCD File
O [auth D],
W [auth H]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
P [auth D],
X [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.245 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.75α = 90
b = 192.47β = 105.08
c = 130.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JST CRESTJapanJPMJCR12M4

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Structure summary
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description