4GSP

RIBONUCLEASE T1 COMPLEXED WITH 2',3'-CGPS + 3'-GMP, 7 DAYS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography.

Zegers, I.Loris, R.Dehollander, G.Fattah Haikal, A.Poortmans, F.Steyaert, J.Wyns, L.

(1998) Nat.Struct.Mol.Biol. 5: 280-283

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Here we present a time-resolved crystallographic analysis of the hydrolysis of exo (Sp) guanosine 2',3'-cyclophosphorothioate by RNase T1. The use of a slow substrate and fast crystallization methods made it possible to perform the study with convent ...

    Here we present a time-resolved crystallographic analysis of the hydrolysis of exo (Sp) guanosine 2',3'-cyclophosphorothioate by RNase T1. The use of a slow substrate and fast crystallization methods made it possible to perform the study with conventional data-collection techniques. The results support the idea that the hydrolysis reaction proceeds through a mechanism that is the inverse of the transesterification reaction. In addition, the structures provide an explanation for the differential behavior of RNase T1 towards exo- and endo-cyclic thiophosphates.


    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Belgium. igzegers@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE T1
A
104Aspergillus oryzae (strain ATCC 42149 / RIB 40)Mutation(s): 0 
Gene Names: rntA
EC: 3.1.27.3
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Go to UniProtKB:  P00651
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
3GP
Query on 3GP

Download SDF File 
Download CCD File 
A
GUANOSINE-3'-MONOPHOSPHATE
C10 H14 N5 O8 P
ZDPUTNZENXVHJC-UUOKFMHZSA-N
 Ligand Interaction
SGP
Query on SGP

Download SDF File 
Download CCD File 
A
GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
C10 H12 N5 O6 P S
QZEROIIFJLCOOE-FHIGPPGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.240α = 90.00
b = 51.100β = 90.00
c = 40.450γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-12-02 
  • Released Date: 1998-08-12 
  • Deposition Author(s): Zegers, I., Wyns, L.

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance