4JJF | pdb_00004jjf

Crystal structure of FE-hydrogenase from methanothermobacter marburgensis in complex with 2-naphthylisocyanide

• PDB DOI: https://doi.org/10.2210/pdb4JJF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanothermobacter marburgensis str. Marburg
• Mutation(s): No 


• Deposited: 2013-03-07 Released: 2013-08-07 
• Deposition Author(s): Tamura, H., Warkentin, E., Ermler, U., Shima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.223 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of [fe]-hydrogenase in complex with inhibitory isocyanides: implications for the h2 -activation site.

Tamura, H., Salomone-Stagni, M., Fujishiro, T., Warkentin, E., Meyer-Klaucke, W., Ermler, U., Shima, S.

(2013) Angew Chem Int Ed Engl 52: 9656-9659

• PubMed: 23873755 
• DOI: https://doi.org/10.1002/anie.201305089
• Primary Citation Related Structures: 
  4JJF, 4JJG

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Organizational Affiliation: 
• Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.07 kDa 
• Atom Count: 5,534 
• Modeled Residue Count: 688 
• Deposited Residue Count: 688 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methenyltetrahydromethanopterin hydrogenase	A, B	344	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0  EC: 1.12.98.2
UniProt
Find proteins for P32440 (Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 / Marburg)) Explore P32440  Go to UniProtKB:  P32440

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE9	C [auth A], E [auth B]	iron-guanylyl pyridinol cofactor C21 H23 Fe N6 O13 P S AEHOAZNVUAGELD-VPXBKTNXSA-K
N2I	D [auth A], F [auth B]	N-(naphthalen-2-yl)methanimine C11 H9 N FGRABSHVUNBHIE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.223 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.18	α = 90
b = 141.18	β = 90
c = 96.46	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Tamura, H., Warkentin, E., Ermler, U., Shima, S.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description