5BU4

RIBONUCLEASE T1 COMPLEX WITH 2'GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Conserved water molecules in a large family of microbial ribonucleases.

Loris, R.Langhorst, U.De Vos, S.Decanniere, K.Bouckaert, J.Maes, D.Transue, T.R.Steyaert, J.

(1999) Proteins 36: 117-134

  • DOI: https://doi.org/10.1002/(sici)1097-0134(19990701)36:1<117::aid-prot10>3.0.co;2-h
  • Primary Citation of Related Structures:  
    1BU4, 2BU4, 3BU4, 4BU4, 5BU4

  • PubMed Abstract: 

    We systematically analyzed the crystallographically determined water molecules of all known structures of RNase T1 and compared them to the ordered solvent in a large number of related microbial nucleases. To assess the crystallographers' impact on the interpretation of the solvent structure, we independently refined five validation structures from diffraction data derived from five isomorphous crystals of RNase T1. We also compared the positions of water molecules found in 11 published isomorphous RNase T1 inhibitor complexes. These data suggest that the positions of most of the waters located on the surface of a protein and that are well-determined in the experimental electron density maps are determined primarily by crystal packing forces. Water molecules with less well-defined electron density are in general unique to one or a small number of crystal structures. Only a small number of the well-defined waters are found to be independent of the crystal environment. These waters have a low accessible surface area and B-factor, and tend to be conserved in the crystal structures of a number of evolutionary related ribonucleases as well. A single water molecule is found conserved in all known microbial ribonucleases.


  • Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Sint-Genesius-Rode, Belgium. reloris@vub.ac.be


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (RIBONUCLEASE T1)104Aspergillus oryzaeMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P00651 
Go to UniProtKB:  P00651
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00651
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2GP
Query on 2GP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-2'-MONOPHOSPHATE
C10 H14 N5 O8 P
WTIFIAZWCCBCGE-UUOKFMHZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.47α = 90
b = 48.1β = 90
c = 50.78γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RESTRAINrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description