RCSB PDB - 3H65: The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin

 3H65

The Crystal Structure of C176A Mutated [Fe]-Hydrogenase (Hmd) Holoenzyme in Complex with Methylenetetrahydromethanopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H4MClick on this verticalbar to view detailsBest fitted I2CClick on this verticalbar to view detailsBest fitted DTVClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

The crystal structure of an [Fe]-hydrogenase-substrate complex reveals the framework for H2 activation.

Hiromoto, T.Warkentin, E.Moll, J.Ermler, U.Shima, S.

(2009) Angew Chem Int Ed Engl 48: 6457-6460


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5,10-methenyltetrahydromethanopterin hydrogenase358Methanocaldococcus jannaschiiMutation(s): 1 
Gene Names: hmdMJ0784
EC: 1.12.98.2
UniProt
Find proteins for Q58194 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58194 
Go to UniProtKB:  Q58194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58194
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H4M
Query on H4M

Download Ideal Coordinates CCD File 
G [auth A]5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN
C31 H45 N6 O16 P
GBMIGEWJAPFSQI-UQXKJNEMSA-N
I2C
Query on I2C

Download Ideal Coordinates CCD File 
B [auth A]5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine
C19 H23 N6 O10 P
FVDPDULUWMBTHF-IPKTUIKJSA-N
DTV
Query on DTV

Download Ideal Coordinates CCD File 
F [auth A](2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CMO
Query on CMO

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.63α = 90
b = 97.63β = 90
c = 165.75γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H4MClick on this verticalbar to view detailsBest fitted I2CClick on this verticalbar to view detailsBest fitted DTVClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description