4N01

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 

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

Wu, R.Endres, M.Joachimiak, A.Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic binding protein
A, B
337Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3)Mutation(s): 0 
Find proteins for D1BNS2 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3))
Go to UniProtKB:  D1BNS2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
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, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 107.192α = 90.00
b = 46.330β = 119.62
c = 108.550γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data scaling
PHENIXrefinement
MLPHAREphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release