4RGZ

Crystal structure of recombinant prolidase from Thermococcus sibiricus at P21221 spacegroup


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.,Sect.F 71: 951-957

  • DOI: 10.1107/S2053230X15009498

  • 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 coun ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xaa-Pro aminopeptidase
A, N, 1, e
367Thermococcus sibiricus (strain MM 739 / DSM 12597)Mutation(s): 0 
Find proteins for C6A2N7 (Thermococcus sibiricus (strain MM 739 / DSM 12597))
Go to UniProtKB:  C6A2N7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
1
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
1, A, e, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.221 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 97.600α = 90.00
b = 123.720β = 90.00
c = 136.520γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references