1DHP

DIHYDRODIPICOLINATE SYNTHASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution.

Mirwaldt, C.Korndorfer, I.Huber, R.

(1995) J.Mol.Biol. 246: 227-239

  • DOI: 10.1006/jmbi.1994.0078

  • PubMed Abstract: 
  • The crystal structure of dihydrodipicolinate synthase from E. coli was determined by multiple isomorphous replacement methods. The structure was refined at a resolution of 2.5 A and the final R-factor is 19.6% for 32,190 reflections between 10.0 A an ...

    The crystal structure of dihydrodipicolinate synthase from E. coli was determined by multiple isomorphous replacement methods. The structure was refined at a resolution of 2.5 A and the final R-factor is 19.6% for 32,190 reflections between 10.0 A and 2.5 A and F > 2 sigma (F). The crystallographic asymmetric unit contains two monomers related by approximate 2-fold symmetry. A tetramer with approximate 222 symmetry is built up by crystallographic symmetry. The tetramer is almost planar with no contacts between the subunits related by the non-crystallographic dyad. The active sites are accessible from a wide water-filled channel in the center of the tetramer. The dihydrodipicolinate synthase monomer is composed of two domains. Each polypeptide chain is folded into an 8-fold alpha/beta barrel and a C-terminal alpha-helical domain comprising residues 224 to 292. The fold is similar to that of N-acetylneuraminate lyase. The active site lysine 161 is located in the alpha/beta barrel and has access via two entrances from the C-terminal side of the barrel.


    Related Citations: 
    • Escherichia Coli Dihydrodipicolinate Synthase. Identification of the Active Site and Crystallization
      Laber, B.,Gomis-Ruth, F.X.,Romao, M.J.,Huber, R.
      (1992) Biochem.J. 288: 691


    Organizational Affiliation

    Max-Planck Institut für Biochemie, Martinsried, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDRODIPICOLINATE SYNTHASE
A, B
292Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dapA
EC: 4.3.3.7
Find proteins for P0A6L2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6L2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 122.410α = 90.00
b = 122.410β = 90.00
c = 111.220γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance