5Z40

Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrrolidone-carboxylate peptidase
A, B
218Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: pcpDR_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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RX25
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.895α = 90
b = 46.87β = 105.61
c = 105.293γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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