6Z8O | pdb_00006z8o

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Krypton gas - structure G491A-Kr

PDB DOI: https://doi.org/10.2210/pdb6Z8O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
Expression System: Nitratidesulfovibrio vulgaris str. Hildenborough
Mutation(s): Yes

Deposited: 2020-06-02 Released: 2020-09-09
Deposition Author(s): Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.275 (Depositor), 0.275 (DCC)
R-Value Work:
0.226 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.

Zacarias, S., Temporao, A., Carpentier, P., van der Linden, P., Pereira, I.A.C., Matias, P.M.

(2020) J Biol Inorg Chem 25: 863-874

PubMed: 32865640 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1007/s00775-020-01814-y
Primary Citation Related Structures:
6Z7R, 6Z8J, 6Z8M, 6Z8O, 6Z9G, 6Z9O, 6ZA1

PubMed Abstract:
Hydrogenases are metalloenzymes that catalyse both H ₂ evolution and uptake. They are gas-processing enzymes with deeply buried active sites, so the gases diffuse through channels that connect the active site to the protein surface. The [NiFeSe] hydrogenases are a special class of hydrogenases containing a selenocysteine as a nickel ligand; they are more catalytically active and less O ₂-sensitive than standard [NiFe] hydrogenases. Characterisation of the channel system of hydrogenases is important to understand how the inhibitor oxygen reaches the active site to cause oxidative damage. To this end, crystals of Desulfovibrio vulgaris Hildenborough [NiFeSe] hydrogenase were pressurized with krypton and oxygen, and a method for tracking labile O ₂ molecules was developed, for mapping a hydrophobic channel system similar to that of the [NiFe] enzymes as the major route for gas diffusion.

Organizational Affiliation

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.

Macromolecule Content

Total Structure Weight: 172.45 kDa
Atom Count: 11,863
Modeled Residue Count: 1,517
Deposited Residue Count: 1,534
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, C	283	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0 Gene Names: hysB, DVU_1917 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, selenocysteine-containing	B, D	484	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 1 Gene Names: hysA, DVU_1918 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
6ML Query on 6ML Download:Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A]	BA [auth C], H [auth A]	oxygen-damaged SF4 Fe₄ O₂ S₄ DCVJTSMMUVGUAG-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain H [auth A] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	AA [auth C] E [auth A] F [auth A] G [auth A] Y [auth C] AA [auth C], E [auth A], F [auth A], G [auth A], Y [auth C], Z [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain Y [auth C] Focus chain Z [auth C]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain IA [auth D] SDF format, chain O [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain O [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain O [auth B]	IA [auth D], O [auth B]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain IA [auth D] Focus chain O [auth B] Interactions & Density Focus chain IA [auth D] Focus chain O [auth B]
KR (Subject of Investigation/LOI) Query on KR Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	CA [auth C] DA [auth C] EA [auth C] FA [auth C] GA [auth C] CA [auth C], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth D], OA [auth D], PA [auth D], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	KRYPTON Kr DNNSSWSSYDEUBZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] 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 N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] 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 N [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] SDF format, chain P [auth B] MOL2 format, chain JA [auth D] MOL2 format, chain P [auth B] mmCIF format, chain JA [auth D] mmCIF format, chain P [auth B]	JA [auth D], P [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Focus chain P [auth B] Interactions & Density Focus chain JA [auth D] Focus chain P [auth B]
FE2 Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain KA [auth D] SDF format, chain Q [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B] mmCIF format, chain KA [auth D] mmCIF format, chain Q [auth B]	KA [auth D], Q [auth B]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain KA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain KA [auth D] Focus chain Q [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain MA [auth D] SDF format, chain S [auth B] MOL2 format, chain MA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain MA [auth D] mmCIF format, chain S [auth B]	MA [auth D], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain MA [auth D] Focus chain S [auth B] Interactions & Density Focus chain MA [auth D] Focus chain S [auth B]
H2S Query on H2S Download:Ideal Coordinates CCD File SDF format, chain LA [auth D] SDF format, chain R [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain R [auth B] mmCIF format, chain LA [auth D] mmCIF format, chain R [auth B]	LA [auth D], R [auth B]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Focus chain R [auth B] Interactions & Density Focus chain LA [auth D] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.275 (Depositor), 0.275 (DCC)
R-Value Work: 0.226 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.716	α = 90
b = 97.022	β = 104.656
c = 121.318	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	PTDC/BBB-BEP/2885/2014
Fundacao para a Ciencia e a Tecnologia	Portugal	LISBOA-01-0145-FEDER-007660

Revision History (Full details and data files)

Version 1.0: 2020-09-09
Type: Initial release
Version 1.1: 2020-09-16
Changes: Database references
Version 1.2: 2020-09-30
Changes: Database references
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Refinement description