2RIR

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis.

Osipiuk, J.Quartey, P.Moy, S.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipicolinate synthase, A chain
A, B, C, D, E
A, B, C, D, E, F, G, H
300Bacillus subtilisMutation(s): 0 
Gene Names: spoVFAdpaABSU16730
UniProt
Find proteins for Q04809 (Bacillus subtilis (strain 168))
Explore Q04809 
Go to UniProtKB:  Q04809
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04809
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
M [auth C]
O [auth D]
Q [auth E]
J [auth A],
L [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth F],
T [auth G],
W [auth H]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
N [auth D]
P [auth E]
S [auth G]
I [auth A],
K [auth B],
N [auth D],
P [auth E],
S [auth G],
U [auth H],
V [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 261.578α = 90
b = 75.108β = 119.74
c = 200.464γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-2000data reduction
SHELXDphasing
SOLVEphasing
RESOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description