1UPX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • DOI: 10.1107/s0907444903025861
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROXYLAMINE REDUCTASEA, B544Desulfovibrio desulfuricansMutation(s): 0 
EC: 1.7.99.1
Find proteins for Q01770 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB))
Explore Q01770 
Go to UniProtKB:  Q01770
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSO
Query on FSO

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]IRON/SULFUR/OXYGEN HYBRID CLUSTER
Fe4 O3 S3
NIIPGMCXXHQOSA-LVFFOBLJCB
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SF3
Query on SF3

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]FE4-S3 CLUSTER
Fe4 S3
QQACTBFBZNWJMV-DXQBTJNKAZ
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
I [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.3α = 82.8
b = 61.2β = 73.7
c = 72γ = 87.3
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

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