4KL8 | pdb_00004kl8

High-resolution structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

PDB DOI: https://doi.org/10.2210/pdb4KL8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Desulfomicrobium baculatum, Desulfomicrobium baculatum DSM 4028
Mutation(s): No

Deposited: 2013-05-07 Released: 2013-07-10
Deposition Author(s): Volbeda, A., Cavazza, C., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free:
0.171 (Depositor), 0.156 (DCC)
R-Value Work:
0.122 (Depositor)
R-Value Observed:
0.124 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase.

Volbeda, A., Amara, P., Iannello, M., De Lacey, A.L., Cavazza, C., Fontecilla-Camps, J.C.

(2013) Chem Commun (Camb) 49: 7061-7063

PubMed: 23811828 Search on PubMed
DOI: https://doi.org/10.1039/c3cc43619e
Primary Citation Related Structures:
4KL8, 4KN9, 4KO1, 4KO2, 4KO3, 4KO4

PubMed Abstract:
This study shows how the NiFeSe site of an anaerobically purified O2-resistant hydrogenase reacts with air to give a seleninate as the first product. Less oxidized states of the active site are readily reduced in the presence of X-rays. Reductive enzyme activation requires an efficient pathway for water escape.

Organizational Affiliation

Metalloproteins Unit, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Grenoble Alpes UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France. anne.volbeda@ibs.fr

Macromolecule Content

Total Structure Weight: 175.69 kDa
Atom Count: 14,237
Modeled Residue Count: 1,540
Deposited Residue Count: 1,568
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 [auth S], C [auth T]	283	Desulfomicrobium baculatum	Mutation(s): 0 EC: 1.12.99.6
UniProt
Find proteins for P13063 (Desulfomicrobium baculatum) Explore P13063 Go to UniProtKB: P13063
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13063
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nickel-dependent hydrogenase large subunit	B [auth L], D [auth M]	499	Desulfomicrobium baculatum DSM 4028	Mutation(s): 0 EC: 1.12.99.6
UniProt
Find proteins for C7LN88 (Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378 / X)) Explore C7LN88 Go to UniProtKB: C7LN88
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7LN88
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain S [auth T] SDF format, chain R [auth T] SDF format, chain Q [auth T] SDF format, chain G [auth S] SDF format, chain F [auth S] SDF format, chain E [auth S] MOL2 format, chain S [auth T] MOL2 format, chain R [auth T] MOL2 format, chain Q [auth T] MOL2 format, chain G [auth S] MOL2 format, chain F [auth S] MOL2 format, chain E [auth S] mmCIF format, chain S [auth T] mmCIF format, chain R [auth T] mmCIF format, chain Q [auth T] mmCIF format, chain G [auth S] mmCIF format, chain F [auth S] mmCIF format, chain E [auth S]	E [auth S] F [auth S] G [auth S] Q [auth T] R [auth T] E [auth S], F [auth S], G [auth S], Q [auth T], R [auth T], S [auth T]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth S] Focus chain F [auth S] Focus chain G [auth S] Focus chain Q [auth T] Focus chain R [auth T] Focus chain S [auth T] Interactions & Density Focus chain E [auth S] Focus chain F [auth S] Focus chain G [auth S] Focus chain Q [auth T] Focus chain R [auth T] Focus chain S [auth T]
FCO Query on FCO Download:Ideal Coordinates CCD File SDF format, chain W [auth M] SDF format, chain M [auth L] MOL2 format, chain W [auth M] MOL2 format, chain M [auth L] mmCIF format, chain W [auth M] mmCIF format, chain M [auth L]	M [auth L], W [auth M]	CARBONMONOXIDE-(DICYANO) IRON C₃ Fe N₂ O VBQUCMTXYFMTTE-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Focus chain W [auth M] Interactions & Density Focus chain M [auth L] Focus chain W [auth M]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth S] SDF format, chain J [auth S] SDF format, chain BA [auth M] SDF format, chain AA [auth M] MOL2 format, chain K [auth S] MOL2 format, chain J [auth S] MOL2 format, chain BA [auth M] MOL2 format, chain AA [auth M] mmCIF format, chain K [auth S] mmCIF format, chain J [auth S] mmCIF format, chain BA [auth M] mmCIF format, chain AA [auth M]	AA [auth M], BA [auth M], J [auth S], K [auth S]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth M] Focus chain J [auth S] Focus chain K [auth S] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth M] Focus chain J [auth S] Focus chain K [auth S]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain X [auth M] SDF format, chain N [auth L] MOL2 format, chain X [auth M] MOL2 format, chain N [auth L] mmCIF format, chain X [auth M] mmCIF format, chain N [auth L]	N [auth L], X [auth M]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain N [auth L] Focus chain X [auth M] Interactions & Density Focus chain N [auth L] Focus chain X [auth M]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth M] SDF format, chain V [auth T] SDF format, chain U [auth T] SDF format, chain T SDF format, chain O [auth L] SDF format, chain L [auth S] SDF format, chain H [auth S] SDF format, chain CA [auth M] MOL2 format, chain Y [auth M] MOL2 format, chain V [auth T] MOL2 format, chain U [auth T] MOL2 format, chain T MOL2 format, chain O [auth L] MOL2 format, chain L [auth S] MOL2 format, chain H [auth S] MOL2 format, chain CA [auth M] mmCIF format, chain Y [auth M] mmCIF format, chain V [auth T] mmCIF format, chain U [auth T] mmCIF format, chain T mmCIF format, chain O [auth L] mmCIF format, chain L [auth S] mmCIF format, chain H [auth S] mmCIF format, chain CA [auth M]	CA [auth M] H [auth S] L [auth S] O [auth L] T CA [auth M], H [auth S], L [auth S], O [auth L], T, U [auth T], V [auth T], Y [auth M]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth M] Focus chain H [auth S] Focus chain L [auth S] Focus chain O [auth L] Focus chain T Focus chain U [auth T] Focus chain V [auth T] Focus chain Y [auth M] Interactions & Density Focus chain CA [auth M] Focus chain H [auth S] Focus chain L [auth S] Focus chain O [auth L] Focus chain T Focus chain U [auth T] Focus chain V [auth T] Focus chain Y [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth S] MOL2 format, chain I [auth S] mmCIF format, chain I [auth S]	I [auth S]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth S] Interactions & Density Focus chain I [auth S]
H2S Query on H2S Download:Ideal Coordinates CCD File SDF format, chain P [auth L] SDF format, chain Z [auth M] MOL2 format, chain P [auth L] MOL2 format, chain Z [auth M] mmCIF format, chain P [auth L] mmCIF format, chain Z [auth M]	P [auth L], Z [auth M]	HYDROSULFURIC ACID H₂ S RWSOTUBLDIXVET-UHFFFAOYSA-N		Interactions Focus chain P [auth L] Focus chain Z [auth M] Interactions & Density Focus chain P [auth L] Focus chain Z [auth M]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SE7 Query on SE7	B [auth L], D [auth M]	L-PEPTIDE LINKING	C₃ H₇ N O₄ Se		SEC
UOX Query on UOX	B [auth L], D [auth M]	L-PEPTIDE LINKING	C₃ H₆ N O₃ Se		SEC

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.171 (Depositor), 0.156 (DCC)
R-Value Work: 0.122 (Depositor)
R-Value Observed: 0.124 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.2	α = 90
b = 108.72	β = 90
c = 136.62	γ = 90

Software Package:

Software Name	Purpose
Xnemo	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Volbeda, A.

Cavazza, C.

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2013-07-24
Changes: Database references
Version 1.3: 2013-12-25
Changes: Other
Version 1.4: 2014-04-09
Changes: Other
Version 1.5: 2014-08-06
Changes: Other
Version 1.6: 2016-06-15
Changes: Non-polymer description
Version 2.0: 2019-05-08
Changes: Advisory, Data collection, Derived calculations, Polymer sequence
Version 3.0: 2022-10-26
Changes: Advisory, Database references, Derived calculations, Non-polymer description
Version 3.1: 2023-09-20
Changes: Data collection, Refinement description