3ZE6 | pdb_00003ze6

3D structure of the Ni-Fe-Se hydrogenase from D. vulgaris Hildenborough in the as-isolated oxidized state at 1.50 Angstroms

PDB DOI: https://doi.org/10.2210/pdb3ZE6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): No

Deposited: 2012-12-03 Released: 2013-06-12
Deposition Author(s): Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.154 (Depositor), 0.148 (DCC)
R-Value Work:
0.135 (Depositor), 0.129 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 4.2 of the entry. See complete history.

Literature

Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough

Marques, M.C., Coelho, R., Pereira, I.A.C., Matias, P.M.

(2013) Int J Hydrogen Energy

DOI: https://doi.org/10.1016/J.IJHYDENE.2013.04.132

Macromolecule Content

Total Structure Weight: 87.2 kDa
Atom Count: 6,804
Modeled Residue Count: 758
Deposited Residue Count: 767
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT	A	283	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS4 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS4 Go to UniProtKB: Q72AS4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72AS4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYS SELENOCYSTEINE-CONTAINING	B	484	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 EC: 1.12.7.2 (PDB Primary Data), 1.12.2.1 (UniProt)
UniProt
Find proteins for Q72AS3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72AS3 Go to UniProtKB: Q72AS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72AS3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSX Query on FSX 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]	BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) Fe₄ O₃ S₃ BIOGFUMNBIDAOG-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		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]
SBY Query on SBY Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	G [auth A], H [auth A], N [auth B], O [auth B], P [auth B]	3-[DODECYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE C₁₇ H₃₇ N O₃ S IZWSFJTYBVKZNK-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS
OCS Query on OCS	B	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS
PSW Query on PSW	B	L-PEPTIDE LINKING	C₃ H₇ N O₂ S Se		SEC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.154 (Depositor), 0.148 (DCC)
R-Value Work: 0.135 (Depositor), 0.129 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.17	α = 90
b = 97.35	β = 90
c = 102.97	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-06-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-06-12
Type: Initial release
Version 1.1: 2013-10-02
Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
Version 1.2: 2014-11-05
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.0: 2019-04-24
Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Other, Polymer sequence
Version 3.0: 2020-06-03
Changes: Atomic model, Derived calculations, Other
Version 4.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 4.1: 2023-12-20
Changes: Refinement description
Version 4.2: 2025-10-01
Changes: Derived calculations, Structure summary