4U9H

Ultra High Resolution Structure Of The Ni-R State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.096 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.

Ogata, H.Nishikawa, K.Lubitz, W.

(2015) Nature 520: 571-574

  • DOI: 10.1038/nature14110
  • Primary Citation of Related Structures:  
    4U9H, 4U9I

  • PubMed Abstract: 
  • The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution ...

    The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase (∼91.3 kDa molecular mass) at 0.89 Å resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H(-)) bridging the Ni and Fe and a proton (H(+)) attached to the sulphur of a cysteine ligand. The Ni-H(-) and Fe-H(-) bond lengths are 1.58 Å and 1.78Å, respectively. Furthermore, we can assign the Fe-CO and Fe-CN(-) ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis.


    Organizational Affiliation

    Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA [auth S]265Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydADvMF_0271
EC: 1.12.2.1
UniProt
Find proteins for P21853 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21853 
Go to UniProtKB:  P21853
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [auth L]533Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydBDvMF_0270
EC: 1.12.2.1
UniProt
Find proteins for P21852 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21852 
Go to UniProtKB:  P21852
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth S], D [auth S]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
E [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NWN (Subject of Investigation/LOI)
Query on NWN

Download Ideal Coordinates CCD File 
J [auth L]hydrido[hydridonickel(2+)]bis(hydrocyanato-1kappaC)(hydroxymethyl)iron
C3 H4 Fe N2 Ni O
ZUFDVORDBCYGRI-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
T [auth L]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth S] , G [auth S] , H [auth S] , I [auth S] , L , M [auth L] , N [auth L] , O [auth L] , 
F [auth S],  G [auth S],  H [auth S],  I [auth S],  L,  M [auth L],  N [auth L],  O [auth L],  P [auth L],  Q [auth L],  R [auth L],  S [auth L]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.096 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.53α = 90
b = 97.95β = 90
c = 125.85γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BMBFGermany03SF0355C
EU/Energy Network project SOLAR-BelgiumFP7 contract 212508

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Database references