4LJS | pdb_00004ljs

The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008

• PDB DOI: https://doi.org/10.2210/pdb4LJS/pdb

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


• Deposited: 2013-07-05 Released: 2013-07-24 
• Deposition Author(s): Tan, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

The crystal structure of a periplasmic binding protein from Veillonella parvula DSM 2008

Tan, K., 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: 37.31 kDa 
• Atom Count: 2,628 
• Modeled Residue Count: 316 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A	324	Veillonella parvula DSM 2008	Mutation(s): 0  Gene Names: Vpar_0062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.32 Å
• R-Value Free:  0.208 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.994	α = 90
b = 82.994	β = 90
c = 110.419	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Tan, K., Chhor, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary