1BU4

RIBONUCLEASE 1 COMPLEX WITH 2'GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1002/(sici)1097-0134(19990701)36:1<117::aid-prot10>3.0.co;2-h
  • Primary Citation of Related Structures:  
    5BU4, 4BU4, 3BU4, 2BU4, 1BU4

  • 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE T1A104Aspergillus oryzaeMutation(s): 0 
Gene Names: SYNTHETIC GENE
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2GP (Subject of Investigation/LOI)
Query on 2GP

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.51α = 90
b = 48β = 90
c = 50.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance