5D51

Krypton derivatization of an O2-tolerant membrane-bound [NiFe] hydrogenase reveals a hydrophobic gas tunnel network


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Krypton Derivatization of an O2 -Tolerant Membrane-Bound [NiFe] Hydrogenase Reveals a Hydrophobic Tunnel Network for Gas Transport.

Kalms, J.Schmidt, A.Frielingsdorf, S.van der Linden, P.von Stetten, D.Lenz, O.Carpentier, P.Scheerer, P.

(2016) Angew Chem Int Ed Engl 55: 5586-5590

  • DOI: 10.1002/anie.201508976
  • Primary Citation of Related Structures:  
    5D51

  • PubMed Abstract: 
  • [NiFe] hydrogenases are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and f ...

    [NiFe] hydrogenases are metalloenzymes catalyzing the reversible heterolytic cleavage of hydrogen into protons and electrons. Gas tunnels make the deeply buried active site accessible to substrates and inhibitors. Understanding the architecture and function of the tunnels is pivotal to modulating the feature of O2 tolerance in a subgroup of these [NiFe] hydrogenases, as they are interesting for developments in renewable energy technologies. Here we describe the crystal structure of the O2 -tolerant membrane-bound [NiFe] hydrogenase of Ralstonia eutropha (ReMBH), using krypton-pressurized crystals. The positions of the krypton atoms allow a comprehensive description of the tunnel network within the enzyme. A detailed overview of tunnel sizes, lengths, and routes is presented from tunnel calculations. A comparison of the ReMBH tunnel characteristics with crystal structures of other O2 -tolerant and O2 -sensitive [NiFe] hydrogenases revealed considerable differences in tunnel size and quantity between the two groups, which might be related to the striking feature of O2 tolerance.


    Organizational Affiliation

    Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany. patrick.scheerer@charite.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uptake hydrogenase large subunitL603Cupriavidus necatorMutation(s): 0 
Gene Names: hoxGPHG002
EC: 1.12.99.6
Find proteins for P31891 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Explore P31891 
Go to UniProtKB:  P31891
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uptake hydrogenase small subunitS339Cupriavidus necatorMutation(s): 0 
Gene Names: hoxKPHG001
EC: 1.12.99.6
Find proteins for P31892 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Explore P31892 
Go to UniProtKB:  P31892
Protein Feature View
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 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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S
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F4S
Query on F4S

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S
FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-UHFFFAOYSA-N
 Ligand Interaction
F3S
Query on F3S

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S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFV
Query on NFV

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L
NI-FE OXIDIZED ACTIVE CENTER
C3 Fe N2 Ni O2
MPQMGFDSXFFIQL-UHFFFAOYSA-N
 Ligand Interaction
KR
Query on KR

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L, S
KRYPTON
Kr
DNNSSWSSYDEUBZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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L, S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.133 
  • R-Value Observed: 0.134 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.387α = 90
b = 95.574β = 90
c = 119.752γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-05-04
    Changes: Database references