3B40

Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa.

Bonanno, J.B.Patskovsky, Y.Dickey, M.Bain, K.T.Mendoza, M.Fong, R.Smith, D.Wasserman, S.Sauder, J.M.Burley, S.K.Almo, S.C.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable dipeptidase
A
417Pseudomonas aeruginosaMutation(s): 11 
Gene Names: pvdM
Find proteins for Q5DIQ1 (Pseudomonas aeruginosa)
Go to UniProtKB:  Q5DIQ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 147.123α = 90.00
b = 147.123β = 90.00
c = 147.123γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SHELXCDphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SHELXEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2018-11-14
    Type: Data collection, Structure summary