2H5Y | pdb_00002h5y

Crystallographic structure of the Molybdate-Binding Protein of Xanthomonas citri at 1.7 Ang resolution bound to molybdate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.202 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Crystallization, data collection and phasing of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri

Santacruz, C.P., Balan, A., Ferreira, L.C., Barbosa, J.A.R.G.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 289-291

  • DOI: https://doi.org/10.1107/S1744309106003812
  • Primary Citation Related Structures: 
    2H5Y

  • PubMed Abstract: 

    Xanthomonas axonopodis pv. citri ModA protein is the ABC periplasmic binding component responsible for the capture of molybdate. The protein was crystallized with sodium molybdate using the hanging-drop vapour-diffusion method in the presence of PEG or sulfate. X-ray diffraction data were collected to a maximum resolution of 1.7 A using synchrotron radiation. The crystal belongs to the orthorhombic space group C222(1), with unit-cell parameters a = 68.15, b = 172.14, c = 112.04 A. The crystal structure was solved by molecular-replacement methods and structure refinement is in progress.

    • Organizational Affiliation: 
    • Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 80.95 kDa 
  • Atom Count: 6,036 
  • Modeled Residue Count: 697 
  • Deposited Residue Count: 762 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Molybdate-binding periplasmic protein
A, B, C
254Xanthomonas citri subsp. citri 306Mutation(s): 0 
Gene Names: modA
UniProt
Find proteins for Q8PHA1 (Xanthomonas axonopodis pv. citri (strain 306))
Explore Q8PHA1 
Go to UniProtKB:  Q8PHA1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8PHA1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.202 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.153α = 90
b = 172.138β = 90
c = 112.036γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description