6AMZ

Crystal structure of a domain swapped 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Crystal structure of a domain swapped 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase from Acinetobacter baumannii

Edwards, T.E., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase281Acinetobacter baumanniiMutation(s): 0 
Gene Names: dapD
EC: 2.3.1.117
UniProt
Find proteins for Q5DL43 (Acinetobacter baumannii)
Explore Q5DL43 
Go to UniProtKB:  Q5DL43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5DL43
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRD
Query on MRD
Download Ideal Coordinates CCD File 
B [auth A](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.158 
  • Space Group: H 3 2
  • Diffraction Data: https://doi.org/10.18430/M36AMZ
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.25α = 90
b = 92.25β = 90
c = 218.44γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description