6HAC | pdb_00006hac

Crystal structure of [Fe]-hydrogenase (Hmd) holoenzyme from Methanococcus aeolicus (open form)

PDB DOI: https://doi.org/10.2210/pdb6HAC/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: 2.30 Å
R-Value Free:
0.192 (Depositor), 0.200 (DCC)
R-Value Work:
0.171 (Depositor), 0.178 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

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: 37.92 kDa
Atom Count: 2,746
Modeled Residue Count: 342
Deposited Residue Count: 342
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5,10-methenyltetrahydromethanopterin hydrogenase	A	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE9 Query on FE9 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]	iron-guanylyl pyridinol cofactor C₂₁ H₂₃ Fe N₆ O₁₃ P S AEHOAZNVUAGELD-VPXBKTNXSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
1PE Query on 1PE 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]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.192 (Depositor), 0.200 (DCC)
R-Value Work: 0.171 (Depositor), 0.178 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.985	α = 90
b = 136.985	β = 90
c = 117.317	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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, Refinement description