4CIP

Spectroscopically-validated structure of ferrous cytochrome c prime from Alcaligenes xylosoxidans, reduced using ascorbate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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.,Sect.D 70: 1289

  • DOI: 10.1107/S1399004714004039
  • Primary Citation of Related Structures:  

  • 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.,Swiss Light Source, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland.,Department of Chemistry and Biochemistry, Eastern Oregon University, La Grande, OR 97850-2899, USA.,Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C'
A
127Alcaligenes xylosoxydans xylosoxydansMutation(s): 0 
Find proteins for P00138 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P00138
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ASC
Query on ASC

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Download CCD File 
A
ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.144 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.716α = 90.00
b = 53.716β = 90.00
c = 180.624γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release