2H5Y

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

• PDB DOI: https://doi.org/10.2210/pdb2H5Y/pdb

• Classification: METAL TRANSPORT
• Organism(s): Xanthomonas citri pv. citri str. 306
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-29 Released: 2007-06-05 
• Deposition Author(s): Balan, A., Santacruz, C.P., Ferreira, L.C.S., Barbosa, J.A.R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Starting Model: experimental

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

• PubMed: 16511325 
• DOI: https://doi.org/10.1107/S1744309106003812
• Primary Citation of 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.

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Organizational Affiliation: 

Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Molybdate-binding periplasmic protein	A, B, C	254	Xanthomonas citri pv. citri str. 306	Mutation(s): 0  Gene Names: modA
UniProt
Find proteins for Q8PHA1 (Xanthomonas axonopodis pv. citri (strain 306)) Explore Q8PHA1  Go to UniProtKB:  Q8PHA1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MOO	F [auth A], H [auth B], J [auth C]	MOLYBDATE ION Mo O4 MEFBJEMVZONFCJ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], G [auth B], I [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.153	α = 90
b = 172.138	β = 90
c = 112.036	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-05 
Deposition Author(s): Balan, A., Santacruz, C.P., Ferreira, L.C.S., Barbosa, J.A.R.G.

Revision History  

• 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