3R5X

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Kim, Y.Hasseman, J.Anderson, W.F.Joachimiak, A.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-alanine--D-alanine ligase
A, B, C, D
307Bacillus anthracisGene Names: ddl (ddlB)
EC: 6.3.2.4
Find proteins for Q81Q29 (Bacillus anthracis)
Go to UniProtKB:  Q81Q29
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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Download CCD File 
D
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 56.336α = 73.36
b = 68.992β = 84.96
c = 92.387γ = 75.46
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXSphasing
BUCCANEERmodel building
HKL-3000data reduction
MLPHAREphasing
PHENIXrefinement
BUCCANEERphasing
HKL-3000data scaling
HKL-3000phasing
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-10-01
    Type: Database references, Structure summary
  • Version 1.3: 2015-06-24
    Type: Other
  • Version 1.4: 2015-07-01
    Type: Derived calculations