1UPX | pdb_00001upx

The crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans containing molecules in the oxidized and reduced states.

PDB DOI: https://doi.org/10.2210/pdb1UPX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Desulfovibrio desulfuricans
Mutation(s): No

Deposited: 2003-10-14 Released: 2003-12-02
Deposition Author(s): Aragao, D., Macedo, S., Mitchell, E.P., Lindley, P.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.153 (Depositor), 0.161 (DCC)
R-Value Work:
0.140 (Depositor), 0.151 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of the Hybrid Cluster Protein (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 Containing Molecules in the Oxidized and Reduced States

Macedo, S., Aragao, D., Mitchell, E.P., Lindley, P.F.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2065

PubMed: 14646063 Search on PubMed
DOI: https://doi.org/10.1107/s0907444903025861
Primary Citation Related Structures:
1UPX

PubMed Abstract:
The hybrid cluster protein (HCP) from the sulfate-reducing bacteria Desulfovibrio desulfuricans ATCC 27774 has been isolated and crystallized anaerobically. The protein sample used in the crystallization studies was several months old, having been stored at 193 K, and initial crystal structure studies were unable to fully resolve details of the hybrid cluster despite the use of high-resolution data to 1.25 A collected at the ESRF, Grenoble, France. Full elucidation of the structure has only become possible with the complete knowledge of the as-isolated and fully reduced crystal structures. The analysis clarifies the significant movements in the position of the Fe atom linked to the persulfide moiety in the oxidized as-isolated protein and the S atom of the persulfide itself as the protein is reduced. The structures of the as-isolated and reduced states are discussed in terms of the putative function of the HCP proteins.

Organizational Affiliation

Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. República, EAN, Apartado 127, 2781-901 Oeiras, Portugal.

Macromolecule Content

Total Structure Weight: 119.46 kDa
Atom Count: 10,132
Modeled Residue Count: 1,088
Deposited Residue Count: 1,088
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYLAMINE REDUCTASE	A, B	544	Desulfovibrio desulfuricans	Mutation(s): 0 EC: 1.7.99.1
UniProt
Find proteins for Q01770 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore Q01770 Go to UniProtKB: Q01770
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01770
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FSO Query on FSO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	IRON/SULFUR/OXYGEN HYBRID CLUSTER Fe₄ O₃ S₃ JQPFOUXUGPAEOB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SF3 Query on SF3 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	FE4-S3 CLUSTER Fe₄ S₃ QQACTBFBZNWJMV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MES Query on MES 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]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.153 (Depositor), 0.161 (DCC)
R-Value Work: 0.140 (Depositor), 0.151 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.3	α = 82.8
b = 61.2	β = 73.7
c = 72	γ = 87.3

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-12-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-12-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Version format compliance
Version 1.2: 2019-05-08
Changes: Advisory, Data collection, Experimental preparation, Other
Version 1.3: 2020-12-23
Changes: Advisory, Derived calculations, Other
Version 1.4: 2023-03-29
Changes: Advisory, Database references, Structure summary
Version 1.5: 2024-02-07
Changes: Data collection, Refinement description