3KB2

Crystal Structure of YorR protein in complex with phosphorylated GDP from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR256


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Northeast Structural Genomics Consortium Target SR256

Forouhar, F.Friedman, D.Seetharaman, J.Janjua, J.Xiao, R.Cunningham, K.Ma, L.Ho, C.Everett, J.K.Nair, R.Acton, T.B.Rost, B.Montelione, G.T.Tong, L.Hunt, J.F.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPBc2 prophage-derived uncharacterized protein yorR
A, B
173Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yorR
Find proteins for O31896 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O31896
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G3D
Query on G3D

Download SDF File 
Download CCD File 
A, B
GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
C10 H16 N5 O14 P3
HEYSFDAMRDTCJM-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-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: 2.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.478α = 90.00
b = 63.050β = 91.57
c = 70.456γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2019-07-17
    Type: Data collection, Derived calculations, Refinement description