4R60 | pdb_00004r60

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris

• PDB DOI: https://doi.org/10.2210/pdb4R60/pdb

• Classification: HYDROLASE
• Organism(s): Xanthomonas campestris pv. campestris str. ATCC 33913
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-22 Released: 2014-09-17 
• Deposition Author(s): Kumar, A., Ghosh, B., Are, V.N., Jamdar, S.N., Makde, R.D., Sharma, S.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris

Kumar, A., Ghosh, B., Are, V.N., Jamdar, S.N., Makde, R.D., Sharma, S.M.

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: 86.08 kDa 
• Atom Count: 6,712 
• Modeled Residue Count: 795 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A, B	400	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 0  Gene Names: pepQ, XCC2409 EC: 3.4.13.9
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MN	D [auth A], E [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	H [auth B], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.324	α = 90
b = 105.515	β = 90
c = 111.352	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Kumar, A., Ghosh, B., Are, V.N., Jamdar, S.N., Makde, R.D., Sharma, S.M.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2016-04-20
  Changes: Other
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description