3I6V

Crystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a periplasmic His/Glu/Gln/Arg/opine family-binding protein from Silicibacter pomeroyi in complex with lysine

Bonanno, J.B.Rutter, M.Bain, K.T.Miller, S.Romero, R.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
periplasmic His/Glu/Gln/Arg/opine family-binding protein
A
232Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)Mutation(s): 0 
Find proteins for Q5LTV6 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Go to UniProtKB:  Q5LTV6
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
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
LYS
Query on LYS

Download SDF File 
Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.931α = 90.00
b = 70.931β = 90.00
c = 141.359γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MAR345data collection
SHELXEmodel building
MOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-11-21
    Type: Data collection, Structure summary