5MAP

X-ray generated oxyferrous complex of DtpA from Streptomyces lividans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Photoreduction and validation of haem-ligand intermediate states in protein crystals by in situ single-crystal spectroscopy and diffraction.

Kekilli, D.Moreno-Chicano, T.Chaplin, A.K.Horrell, S.Dworkowski, F.S.N.Worrall, J.A.R.Strange, R.W.Hough, M.A.

(2017) IUCrJ 4: 263-270

  • DOI: https://doi.org/10.1107/S2052252517002159
  • Primary Citation of Related Structures:  
    5MAP, 5MJH

  • PubMed Abstract: 

    Powerful synergies are available from the combination of multiple methods to study proteins in the crystalline form. Spectroscopies which probe the same region of the crystal from which X-ray crystal structures are determined can give insights into redox, ligand and spin states to complement the information gained from the electron-density maps. The correct assignment of crystal structures to the correct protein redox and ligand states is essential to avoid the misinterpretation of structural data. This is a particular concern for haem proteins, which can occupy a wide range of redox states and are exquisitely sensitive to becoming reduced by solvated electrons generated from interactions of X-rays with water molecules in the crystal. Here, single-crystal spectroscopic fingerprinting has been applied to investigate the laser photoreduction of ferric haem in cytochrome c '. Furthermore, in situ X-ray-driven generation of haem intermediates in crystals of the dye-decolourizing-type peroxidase A (DtpA) from Streptomyces lividans is described.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DtpA
A, B
376Streptomyces lividans TK24Mutation(s): 0 
Gene Names: SLIV_18505
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.786α = 90
b = 70.627β = 93
c = 77.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Leverhulme TrustUnited KingdomRPG-2014-355

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description