5Z40 | pdb_00005z40

Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1

• PDB DOI: https://doi.org/10.2210/pdb5Z40/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-09 Released: 2019-01-16 
• Deposition Author(s): Agrawal, R., Kumar, A., Makde, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.228 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans reveal the mechanism of L-pyroglutamate recognition

Agrawal, R., Ghosh, B., Kumar, A., Makde, R.D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.23 kDa 
• Atom Count: 3,451 
• Modeled Residue Count: 420 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolidone-carboxylate peptidase	A, B	218	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: pcp, DR_0490 EC: 3.4.19.3
UniProt
Find proteins for Q9RX25 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RX25  Go to UniProtKB:  Q9RX25

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.228 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.895	α = 90
b = 46.87	β = 105.61
c = 105.293	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Agrawal, R., Kumar, A., Makde, R.D.

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description