1DHP | pdb_00001dhp

DIHYDRODIPICOLINATE SYNTHASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.197 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1DHP

This is version 1.3 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 Biology 246: 227-239

  • DOI: https://doi.org/10.1006/jmbi.1994.0078
  • Primary Citation Related Structures: 
    1DHP

  • 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 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.


  • Organizational Affiliation
    • Max-Planck Institut für Biochemie, Martinsried, FRG.

Macromolecule Content 

  • Total Structure Weight: 62.69 kDa 
  • Atom Count: 4,726 
  • Modeled Residue Count: 584 
  • Deposited Residue Count: 584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DIHYDRODIPICOLINATE SYNTHASE
A, B
292Escherichia coliMutation(s): 0 
Gene Names: DAPA
EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for P0A6L2 (Escherichia coli (strain K12))
Explore P0A6L2 
Go to UniProtKB:  P0A6L2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6L2
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.41α = 90
b = 122.41β = 90
c = 111.22γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other