4CDV

Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation 3D Report Full Report



Literature

Fingerprinting Redox and Ligand States in Haemprotein Crystal Structures Using Resonance Raman Spectroscopy.

Kekilli, D.Dworkowski, F.S.Pompidor, G.Fuchs, M.R.Andrew, C.R.Antonyuk, S.Strange, R.W.Eady, R.R.Hasnain, S.S.Hough, M.A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1289

  • DOI: 10.1107/S1399004714004039
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularl ...

    It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.


    Organizational Affiliation

    School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'A127Achromobacter xylosoxidansMutation(s): 0 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Explore P00138 
Go to UniProtKB:  P00138
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.281α = 90
b = 53.281β = 90
c = 180.751γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 2.0: 2020-03-11
    Changes: Advisory, Derived calculations, Other, Polymer sequence