6HAE | pdb_00006hae

Crystal structure of [Fe]-hydrogenase (Hmd) from Methanococcus aeolicus in complex with FeGP cofactor and methenyl-tetrahydromethanopterin (close form B)

PDB DOI: https://doi.org/10.2210/pdb6HAE/pdb

Classification: OXIDOREDUCTASE
Organism(s): Methanococcus aeolicus Nankai-3
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-07 Released: 2019-08-28
Deposition Author(s): Huang, G., Wagner, T., Wodrich, M.D., Ataka, K., Bill, E., Ermler, U., Hu, X., Shima, S.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.192 (Depositor), 0.191 (DCC)
R-Value Work:
0.161 (Depositor), 0.159 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The atomic-resolution crystal structure of activated [Fe]-hydrogenase

Huang, G., Wagner, T., Wodrich, M.D., Ataka, K., Bill, E., Ermler, U., Hu, X., Shima, S.

(2019) Nat Catal

DOI: https://doi.org/10.1038/s41929-019-0289-4

Macromolecule Content

Total Structure Weight: 78.26 kDa
Atom Count: 6,029
Modeled Residue Count: 684
Deposited Residue Count: 684
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, B [auth K]	342	Methanococcus aeolicus Nankai-3	Mutation(s): 0 Gene Names: hmd, Maeo_1025 EC: 1.12.98.2
UniProt
Find proteins for A6UVT1 (Methanococcus aeolicus (strain ATCC BAA-1280 / DSM 17508 / OCM 812 / Nankai-3)) Explore A6UVT1 Go to UniProtKB: A6UVT1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6UVT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
E4M Query on E4M Download:Ideal Coordinates CCD File SDF format, chain S [auth K] SDF format, chain D [auth A] MOL2 format, chain S [auth K] MOL2 format, chain D [auth A] mmCIF format, chain S [auth K] mmCIF format, chain D [auth A]	D [auth A], S [auth K]	1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol C₃₁ H₄₄ N₆ O₁₆ P RANKJVUGLXUXOL-CAFBYHECSA-O		Interactions Focus chain D [auth A] Focus chain S [auth K] Interactions & Density Focus chain D [auth A] Focus chain S [auth K]
FE9 Query on FE9 Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain FA [auth K] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth K] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth K]	FA [auth K], Q [auth A]	iron-guanylyl pyridinol cofactor C₂₁ H₂₃ Fe N₆ O₁₃ P S AEHOAZNVUAGELD-VPXBKTNXSA-K		Interactions Focus chain FA [auth K] Focus chain Q [auth A] Interactions & Density Focus chain FA [auth K] Focus chain Q [auth A]
2PE Query on 2PE Download:Ideal Coordinates CCD File SDF format, chain EA [auth K] MOL2 format, chain EA [auth K] mmCIF format, chain EA [auth K]	EA [auth K]	NONAETHYLENE GLYCOL C₁₈ H₃₈ O₁₀ YZUUTMGDONTGTN-UHFFFAOYSA-N		Interactions Focus chain EA [auth K] Interactions & Density Focus chain EA [auth K]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth K] SDF format, chain C [auth A] MOL2 format, chain R [auth K] MOL2 format, chain C [auth A] mmCIF format, chain R [auth K] mmCIF format, chain C [auth A]	C [auth A], R [auth K]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain R [auth K] Interactions & Density Focus chain C [auth A] Focus chain R [auth K]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain Z [auth K] SDF format, chain Y [auth K] SDF format, chain X [auth K] SDF format, chain W [auth K] SDF format, chain V [auth K] SDF format, chain U [auth K] SDF format, chain M [auth A] SDF format, chain L [auth A] 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] SDF format, chain F [auth A] SDF format, chain AA [auth K] MOL2 format, chain Z [auth K] MOL2 format, chain Y [auth K] MOL2 format, chain X [auth K] MOL2 format, chain W [auth K] MOL2 format, chain V [auth K] MOL2 format, chain U [auth K] MOL2 format, chain M [auth A] MOL2 format, chain L [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] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth K] mmCIF format, chain Y [auth K] mmCIF format, chain X [auth K] mmCIF format, chain W [auth K] mmCIF format, chain V [auth K] mmCIF format, chain U [auth K] mmCIF format, chain M [auth A] mmCIF format, chain L [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] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth K]	AA [auth K] F [auth A] G [auth A] H [auth A] I [auth A] AA [auth K], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], U [auth K], V [auth K], W [auth K], X [auth K], Y [auth K], Z [auth K]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain AA [auth K] Focus chain F [auth A] 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] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth K] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K] Focus chain Y [auth K] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain F [auth A] 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] Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth K] Focus chain V [auth K] Focus chain W [auth K] Focus chain X [auth K] Focus chain Y [auth K] Focus chain Z [auth K]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain DA [auth K] SDF format, chain CA [auth K] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth K] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth K]	CA [auth K], DA [auth K], O [auth A], P [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth K] Focus chain DA [auth K] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain CA [auth K] Focus chain DA [auth K] Focus chain O [auth A] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain BA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth K]	BA [auth K], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth K] Focus chain N [auth A] Interactions & Density Focus chain BA [auth K] Focus chain N [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth K] SDF format, chain E [auth A] MOL2 format, chain T [auth K] MOL2 format, chain E [auth A] mmCIF format, chain T [auth K] mmCIF format, chain E [auth A]	E [auth A], T [auth K]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain T [auth K] Interactions & Density Focus chain E [auth A] Focus chain T [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.192 (Depositor), 0.191 (DCC)
R-Value Work: 0.161 (Depositor), 0.159 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.015	α = 90
b = 156.48	β = 90
c = 53.654	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2019-08-28
Type: Initial release
Version 1.1: 2019-09-04
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description