5DYR

Structure of virulence-associated protein D (VapD) from Xylella fastidiosa

• PDB DOI: https://doi.org/10.2210/pdb5DYR/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Xylella fastidiosa 9a5c
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-25 Released: 2016-01-27 
• Deposition Author(s): Kochneva, M.V., dos Santos, M.L., dos Santos, C.A., de Souza, A.P., Polikarpov, I., Aparicio, R., Golubev, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Structure of virulence-associated protein D (VapD) from Xylella fastidiosa

Kochneva, M.V., dos Santos, M.L., dos Santos, C.A., de Souza, A.P., Polikarpov, I., Aparicio, R., Golubev, A.M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.66 kDa 
• Atom Count: 1,174 
• Modelled Residue Count: 139 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virulence-associated protein D	A	151	Xylella fastidiosa 9a5c	Mutation(s): 0  Gene Names: XF_a0052
UniProt
Find proteins for Q9PHF6 (Xylella fastidiosa (strain 9a5c)) Explore Q9PHF6  Go to UniProtKB:  Q9PHF6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.253 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.93	α = 90
b = 107.93	β = 90
c = 53.281	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
XDS	data scaling
CNS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Kochneva, M.V., dos Santos, M.L., dos Santos, C.A., de Souza, A.P., Polikarpov, I., Aparicio, R., Golubev, A.M.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references