4LJS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic binding proteinA324Veillonella parvula DSM 2008Mutation(s): 0 
Gene Names: Vpar_0062
UniProt
Find proteins for D1BQD8 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / CCUG 5123 / JCM 12972 / NCTC 11810 / Te3))
Explore D1BQD8 
Go to UniProtKB:  D1BQD8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.994α = 90
b = 82.994β = 90
c = 110.419γ = 120
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release