4LJS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.321 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 

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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic binding protein
A
324Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3)Mutation(s): 0 
Find proteins for D1BQD8 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3))
Go to UniProtKB:  D1BQD8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.321 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.154 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 82.994α = 90.00
b = 82.994β = 90.00
c = 110.419γ = 120.00
Software Package:
Software NamePurpose
SHELXDphasing
SBC-Collectdata collection
HKL-3000phasing
WARPmodel building
HKL-3000data reduction
DMphasing
ARPmodel building
PHENIXrefinement
DMmodel building
MLPHAREphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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