3B40

Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable dipeptidaseA417Pseudomonas aeruginosaMutation(s): 11 
Gene Names: pvdMPA2393IPC1481_29865IPC1509_30695IPC620_21025
Find proteins for Q5DIQ1 (Pseudomonas aeruginosa)
Explore Q5DIQ1 
Go to UniProtKB:  Q5DIQ1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.123α = 90
b = 147.123β = 90
c = 147.123γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building

Structure Validation

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Entry History 

Revision History 

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