3F47

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 3F47

Classification: OXIDOREDUCTASE

Total Structure Weight: 39400.32

Macromolecule Entities
Molecule Chains Length Organism Details
5,10-methenyltetrahydromethanopterin hydrogenase A 358 Methanocaldococcus jannaschii EC#: 1.12.98.2 IUBMB
Gene Name(s): hmd MJ0784
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
I2C
Query on I2C

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
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CMO
Query on CMO

A CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.205
  • R-Value Work: 0.173
  • Space Group: I 41 2 2

Unit Cell:

Length (Å) Angle (°)
a = 95.93 α = 90.00
b = 95.93 β = 90.00
c = 165.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-10-31
  • Released Date: 2009-02-10
  • Deposition author(s): Hiromoto, T., Pilak, O., Warkentin, E., Thauer, R.K., Shima, S., Ermler, U.

Revision History

  • Version 1_0: 2009-02-10

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Advisory, Version format compliance

  • Version 1_2: 2017-10-25

    Type: Refinement description