3KNZ | pdb_00003knz

Crystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella typhimurium LT2 at 2.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3KNZ/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-12 Released: 2009-12-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella typhimurium LT2 at 2.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 247.26 kDa 
• Atom Count: 15,298 
• Modeled Residue Count: 1,925 
• Deposited Residue Count: 2,196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sugar binding protein	A, B, C, D, E, F	366	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: STM0573
UniProt
Find proteins for Q8ZR49 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZR49  Go to UniProtKB:  Q8ZR49

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETX	G [auth A], J [auth D]	2-ETHOXYETHANOL C4 H10 O2 ZNQVEEAIQZEUHB-UHFFFAOYSA-N
IMD	H [auth A], I [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33KNZ

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.028	α = 90
b = 173.344	β = 90
c = 208.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary