5CDE | pdb_00005cde

R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris

• PDB DOI: https://doi.org/10.2210/pdb5CDE/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-07-03 Released: 2016-09-14 
• Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.224 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris at 1.85 Angstrom resolution

Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.01 kDa 
• Atom Count: 6,536 
• Modeled Residue Count: 795 
• Deposited Residue Count: 796 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A, B	398	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1  Gene Names: pepQ, XCC2409
UniProt
Find proteins for Q8P839 (Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25)) Explore Q8P839  Go to UniProtKB:  Q8P839

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.224 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.088	α = 90
b = 101.947	β = 90
c = 111.509	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
RESOLVE	phasing
SOLVE	phasing
Aimless	data scaling
XDS	data processing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations