5J7N | pdb_00005j7n

Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high order structure

• PDB DOI: https://doi.org/10.2210/pdb5J7N/pdb

• Classification: CHAPERONE
• Organism(s): Xylella fastidiosa 9a5c
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-06 Released: 2017-04-12 
• Deposition Author(s): Fonseca, E.M.B., Scorsato, V., dos Santos, C.A., Tomazini Jr., A., Aparicio, R., Polikarpov, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.

Fonseca, E.M., Scorsato, V., Dos Santos, M.L., Junior, A.T., Tada, S.F., Dos Santos, C.A., de Toledo, M.A., de Souza, A.P., Polikarpov, I., Aparicio, R.

(2017) Acta Crystallogr F Struct Biol Commun 73: 222-227

• PubMed: 28368281 
• DOI: https://doi.org/10.1107/S2053230X17004101
• Primary Citation Related Structures: 
  5J7N


• PubMed Abstract: 
  

  Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.

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Organizational Affiliation: 
• Laboratory of Structural Biology and Crystallography, Institute of Chemistry, University of Campinas, CP6154, 13083-970 Campinas-SP, Brazil.
Molecular Biotechnology Group, Department of Physics and Interdisciplinary Science, Sao Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Avenida Trabalhador São-carlense 400, Parque Arnold Schimidt, 13566-590 São Carlos-SP, Brazil.
Laboratory of Molecular and Genetic Analysis, Center for Molecular Biology and Genetic Engineering, Institute of Biology, University of Campinas, CP6010, 13083-875 Campinas-SP, Brazil.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.88 kDa 
• Atom Count: 857 
• Modeled Residue Count: 109 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight heat shock protein	A	160	Xylella fastidiosa 9a5c	Mutation(s): 0  Gene Names: XF_2234
UniProt
Find proteins for Q9PBB0 (Xylella fastidiosa (strain 9a5c)) Explore Q9PBB0  Go to UniProtKB:  Q9PBB0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.94	α = 90
b = 68.94	β = 90
c = 72.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
MOSFLM	data reduction
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Fonseca, E.M.B., Scorsato, V., dos Santos, C.A., Tomazini Jr., A., Aparicio, R., Polikarpov, I.

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description