Macromolecule Content

Total Structure Weight: 77.07 kDa
Atom Count: 5534
Modelled Residue Count: 688
Deposited Residue Count: 688
Unique protein chains: 1

4JJF

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

PDB DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.171
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
DOI: 10.1002/anie.201305089
Primary Citation of Related Structures:
4JJF, 4JJG

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methenyltetrahydromethanopterin hydrogenase	A, B	344	Methanothermobacter marburgensis str. Marburg	Mutation(s): 0 Gene Names: hmd, mth, MTBMA_c15260 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32440
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE9 Query on FE9 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	iron-guanylyl pyridinol cofactor C₂₁ H₂₃ Fe N₆ O₁₃ P S AEHOAZNVUAGELD-VPXBKTNXSA-K		Ligand Interaction
N2I Query on N2I Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	N-(naphthalen-2-yl)methanimine C₁₁ H₉ N FGRABSHVUNBHIE-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
N2I	PDBBind: 4JJF	Ki: 10 (nM) from 1 assay(s)
N2I	Binding MOAD: 4JJF	Ki: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223
R-Value Work: 0.171
R-Value Observed: 0.173
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2013-03-07
Released Date: 2013-08-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2013-09-18
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.