4RGZ

Crystal structure of recombinant prolidase from Thermococcus sibiricus at P21221 spacegroup


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of recombinant prolidase from Thermococcus sibiricus in space group P21221.

Timofeev, V.Slutskaya, E.Gorbacheva, M.Boyko, K.Rakitina, T.Korzhenevskiy, D.Lipkin, A.Popov, V.

(2015) Acta Crystallogr F Struct Biol Commun 71: 951-957

  • DOI: https://doi.org/10.1107/S2053230X15009498
  • Primary Citation of Related Structures:  
    4RGZ

  • PubMed Abstract: 

    The crystal structure of recombinant prolidase from Thermococcus sibiricus was determined by X-ray diffraction at a resolution of 2.6 Å and was found to contain a tetramer in the asymmetric unit. A protein crystal grown in microgravity using the counter-diffusion method was used for X-ray studies. The crystal belonged to space group P21221, with unit-cell parameters a = 97.60, b = 123.72, c = 136.52 Å, α = β = γ = 90°. The structure was refined to an Rcryst of 22.1% and an Rfree of 29.6%. The structure revealed flexible folding of the N-terminal domain of the protein as well as high variability in the positions of the bound metal ions. The coordinates of the resulting model were deposited in the Protein Data Bank as entry 4rgz.


  • Organizational Affiliation

    Protein Factory, National Research Centre `Kurchatov Institute', Akademika Kurchatova Square 1, Moscow 123182, Russian Federation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xaa-Pro aminopeptidaseA,
B [auth N],
C [auth 1],
D [auth e]
367Thermococcus sibiricus MM 739Mutation(s): 0 
Gene Names: TSIB_0821
UniProt
Find proteins for C6A2N7 (Thermococcus sibiricus (strain DSM 12597 / MM 739))
Explore C6A2N7 
Go to UniProtKB:  C6A2N7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6A2N7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth 1],
K [auth 1],
M [auth 1]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth N]
H [auth N]
I [auth 1]
E [auth A],
F [auth A],
G [auth N],
H [auth N],
I [auth 1],
L [auth 1],
N [auth e],
O [auth e]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.6α = 90
b = 123.72β = 90
c = 136.52γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-30
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Experimental preparation