3H65 | pdb_00003h65

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

PDB DOI: https://doi.org/10.2210/pdb3H65/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-23 Released: 2009-09-01
Deposition Author(s): Hiromoto, T., Warkentin, E., Shima, S., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.173 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 19623593 Search on PubMed
DOI: https://doi.org/10.1002/anie.200902695
Primary Citation Related Structures:
3H65

Organizational Affiliation

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.

Macromolecule Content

Total Structure Weight: 40.29 kDa
Atom Count: 2,850
Modeled Residue Count: 345
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methenyltetrahydromethanopterin hydrogenase	A	358	Methanocaldococcus jannaschii	Mutation(s): 1 Gene Names: hmd, MJ0784 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q58194
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H4M Query on H4M Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN C₃₁ H₄₅ N₆ O₁₆ P GBMIGEWJAPFSQI-UQXKJNEMSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
I2C Query on I2C Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DTV Query on DTV Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-QWWZWVQMSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]