4MO9

Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.925 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of TroA-like Periplasmic Binding Protein FepB from Veillonella parvula

Kim, Y.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
369Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3)Mutation(s): 0 
Find proteins for D1BQR9 (Veillonella parvula (strain ATCC 10790 / DSM 2008 / JCM 12972 / Te3))
Go to UniProtKB:  D1BQR9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
TMO
Query on TMO

Download SDF File 
Download CCD File 
A
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-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: 1.925 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.402α = 90.00
b = 75.999β = 90.00
c = 125.187γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXrefinement
MLPHAREphasing
HKL-3000data scaling
ARP/wARPmodel building
SBC-Collectdata collection
DMphasing
DMmodel building
SHELXSphasing
HKL-3000data reduction
HKL-3000phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description