Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.50 kDa 
• Atom Count: 877 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

3BU4

RIBONUCLEASE T1 COMPLEX WITH 2'GMP

• PDB DOI: 10.2210/pdb3BU4/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-09-14 Released: 1998-09-23 
• Deposition Author(s): Loris, R., Devos, S., Langhorst, U., Decanniere, K., Bouckaert, J., Maes, D., Transue, T.R., Steyaert, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

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

• PubMed: 10373011 
• DOI: 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.

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Organizational Affiliation: 

Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Sint-Genesius-Rode, Belgium. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RIBONUCLEASE T1)	A	104	Aspergillus oryzae	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2GP	C [auth A]	GUANOSINE-2'-MONOPHOSPHATE C10 H14 N5 O8 P WTIFIAZWCCBCGE-UUOKFMHZSA-N
CA	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: 0.249 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.48	α = 90
b = 48.1	β = 90
c = 50.77	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-09-14 
• Released Date: 1998-09-23 
Deposition Author(s): Loris, R., Devos, S., Langhorst, U., Decanniere, K., Bouckaert, J., Maes, D., Transue, T.R., Steyaert, J.

Revision History  

• 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