5CIK | pdb_00005cik

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition

• PDB DOI: https://doi.org/10.2210/pdb5CIK/pdb

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


• Deposited: 2015-07-13 Released: 2016-07-20 
• Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Agrawal, U., Jamdar, S., Makde, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition

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

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: 86.18 kDa 
• Atom Count: 6,610 
• Modeled Residue Count: 794 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proline dipeptidase	A, B	399	Xanthomonas campestris pv. campestris str. ATCC 33913	Mutation(s): 1  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], F [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.181 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.179	α = 90
b = 103.673	β = 90
c = 136.063	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
PHENIX	model building
PHASER	phasing
XDS	data processing
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Agrawal, U., Jamdar, S., Makde, R.D.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2018-07-04
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description