6H63 | pdb_00006h63

Semisynthetic [FeFe]-hydrogenase CpI with ethanedithiolate [2Fe] cofactor

PDB DOI: https://doi.org/10.2210/pdb6H63/pdb

Classification: OXIDOREDUCTASE
Organism(s): Clostridium pasteurianum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-07-26 Released: 2019-09-18
Deposition Author(s): Duan, J., Winkler, M., Hofmann, E., Happe, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.245 (Depositor), 0.247 (DCC)
R-Value Work:
0.201 (Depositor), 0.205 (DCC)
R-Value Observed:
0.203 (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

Geometry of the Catalytic Active Site in [FeFe]-Hydrogenase Is Determined by Hydrogen Bonding and Proton Transfer

Duan, J., Mebs, S., Laun, K., Wittkamp, F., Heberle, J., Happe, T., Hofmann, E., Apfel, U.-P., Winkler, M., Senger, M., Haumann, M., Stripp, S.

(2019) ACS Catal

DOI: https://doi.org/10.1021/acscatal.9b02203

Macromolecule Content

Total Structure Weight: 134.14 kDa
Atom Count: 9,888
Modeled Residue Count: 1,154
Deposited Residue Count: 1,168
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron hydrogenase 1	A, B	584	Clostridium pasteurianum	Mutation(s): 0 EC: 1.12.7.2
UniProt
Find proteins for P29166 (Clostridium pasteurianum) Explore P29166 Go to UniProtKB: P29166
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] L [auth B] D [auth A], E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]
FU8 Query on FU8 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	dicarbonyl[bis(cyanide-kappaC)]-mu-(ethanethiolatato-1kappaS:2kappaS)-mu-(ox omethylidene)diiron(2+) C₇ H₄ Fe₂ N₂ O₃ S₂ MZEMAHMYMVUPIF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B]	H [auth A], P [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B]	I [auth A], J [auth A], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.245 (Depositor), 0.247 (DCC)
R-Value Work: 0.201 (Depositor), 0.205 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.02	α = 90
b = 73.53	β = 97.66
c = 104.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-18
Type: Initial release
Version 1.1: 2020-03-11
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description