3K0T

Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas syringae pv. tomato str. DC3000

• PDB DOI: https://doi.org/10.2210/pdb3K0T/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas syringae pv. tomato
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-25 Released: 2010-06-16 
• Deposition Author(s): Zhang, H.M., Li, M., Chang, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Crystal structure of the PSPTO-PSP protein from Pseudomonas syringae pv. tomato str. DC3000 in complex with D-glucose

Zhang, H.M., Gao, Y., Li, M., Chang, W.R.

(2010) Biochem Biophys Res Commun 397: 82-86

• PubMed: 20478270 
• DOI: https://doi.org/10.1016/j.bbrc.2010.05.071
• Primary Citation of Related Structures:  
  3K0T


• PubMed Abstract: 
  

  The perchloric acid-soluble protein (PSP) is an endoribonuclease and on the basis of sequence similarity has been assigned to the YjgF/YER057c/UK114 family. These family members are ubiquitous and highly conserved in evolution, and participate in regulating basic cellular metabolism. Here we present the 2.1A crystal structure of the PSP protein from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO-PSP), in complex with D-glucose. The quaternary structure of PSPTO-PSP is a homologous trimer. Glucose is located in the cavity between each two monomers. Comparison of the hydrogen bonds between ligands and YjgF/YER057c/UK114 family homologues confirms that the conserved Arg(103) of PSPTO-PSP is a key amino acid in this cavity for ligand binding. It indicated that the involvement of PSPTO-PSP in essential cellular mechanism was regulated by glucose occupying this active site.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, PR China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 47.65 kDa 
• Atom Count: 3,033 
• Modelled Residue Count: 370 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoribonuclease L-PSP, putative	A, B, C	143	Pseudomonas syringae pv. tomato	Mutation(s): 0  Gene Names: PSPTO0072
UniProt
Find proteins for Q88BE5 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q88BE5  Go to UniProtKB:  Q88BE5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	D [auth A], E [auth B], F [auth C]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.237 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.896	α = 90
b = 75.714	β = 90
c = 79.304	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Zhang, H.M., Li, M., Chang, W.R.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary