3B40

Crystal structure of the probable dipeptidase PvdM from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb3B40/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-10-23 Released: 2007-11-06 
• Deposition Author(s): 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., New York SGX Research Center for Structural Genomics (NYSGXRC)

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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 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.14 kDa 
• Atom Count: 3,507 
• Modelled Residue Count: 400 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable dipeptidase	A	417	Pseudomonas aeruginosa	Mutation(s): 11  Gene Names: pvdM, PA2393
UniProt
Find proteins for Q5DIQ1 (Pseudomonas aeruginosa) Explore Q5DIQ1  Go to UniProtKB:  Q5DIQ1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 147.123	α = 90
b = 147.123	β = 90
c = 147.123	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-06 
Deposition Author(s): 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., New York SGX Research Center for Structural Genomics (NYSGXRC)

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
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2024-02-21
  Changes: Data collection