6GGU | pdb_00006ggu

Crystal structure of native FE-hydrogenase from Methanothermobacter marburgensis

PDB DOI: https://doi.org/10.2210/pdb6GGU/pdb

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

Deposited: 2018-05-03 Released: 2019-05-22
Deposition Author(s): Wagner, T., Huang, G., Ermler, U., Shima, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.235 (Depositor), 0.257 (DCC)
R-Value Work:
0.188 (Depositor), 0.206 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Self-protection of the catalytic iron center of a methanogenic [Fe]-hydrogenase via a dynamic dimer-to-hexamer transformation

Wagner, T., Huang, G., Ermler, U., Shima, S.

To be published.

Macromolecule Content

Total Structure Weight: 39.32 kDa
Atom Count: 2,799
Modeled Residue Count: 344
Deposited Residue Count: 344
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	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE9 Query on FE9 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]	iron-guanylyl pyridinol cofactor C₂₁ H₂₃ Fe N₆ O₁₃ P S AEHOAZNVUAGELD-VPXBKTNXSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]