4OVK | pdb_00004ovk

Crystal structure of periplasmic solute binding protein from Veillonella parvula DSM 2008

• PDB DOI: https://doi.org/10.2210/pdb4OVK/pdb

• Classification: SOLUTE-BINDING PROTEIN
• Organism(s): Veillonella parvula DSM 2008
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-15 Released: 2013-12-18 
• Deposition Author(s): Chang, C., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Literature

Crystal structure of periplasmic solute binding protein from Veillonella parvula DSM 2008

Chang, C., Chhor, G., Endres, M., Joachimiak, A.

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: 39.19 kDa 
• Atom Count: 2,988 
• Modeled Residue Count: 329 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	341	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0328

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.146	α = 90
b = 58.872	β = 90
c = 113.751	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-18 
Deposition Author(s): Chang, C., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-12-18
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Data collection
• Version 1.2: 2014-01-22
  Changes: Structure summary
• Version 1.3: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2015-02-11
  Changes: Source and taxonomy
• Version 1.5: 2017-09-27
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.6: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.7: 2024-11-06
  Changes: Structure summary