1BEL | pdb_00001bel

HYDROLASE PHOSPHORIC DIESTER, RNA

• PDB DOI: https://doi.org/10.2210/pdb1BEL/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 1995-12-21 Released: 1996-10-14 
• Deposition Author(s): Dung, M.H., Bell, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work: 
  0.150 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Structure of crystal form IX of bovine pancreatic ribonuclease A.

Dung, M.H., Bell, J.A.

(1997) Acta Crystallogr D Biol Crystallogr 53: 419-425

• PubMed: 15299907 
• DOI: https://doi.org/10.1107/S0907444997000929
• Primary Citation of Related Structures:  
  1BEL


• PubMed Abstract: 
  

  The X-ray structure of crystal form IX of bovine pancre- atic ribonuclease A (space group P2(1)2(1)2(1)) is reported at 1.6 A resolution. The structure was refined to an R factor of 15.0% and includes coordinates for two sulfate ions, four methanol molecules and 82 waters. The structure could be superimposed on the highest resolution crystal structure of bovine pancreatic fibonuclease available (in space group P2(1)) with an r.m.s, difference in main-chain atomic positions of 0.51 A. Most of the larger differences between the two structures could be related to crystal lattice contacts. Superposition of the new structure with eight other structures of ribonuclease in six crystal forms resulted in an r.m.s, deviation from the average structure of 0.43 A for all main-chain atoms. This similarity among structures exists in spite of the fact that all nine molecules are in different crystal environments.

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Organizational Affiliation: 

Department of Chemistry and Center for Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.03 kDa 
• Atom Count: 1,051 
• Modelled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE A	A	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MOH	D [auth A], E [auth A], F [auth A], G [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Work:  0.150 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.9	α = 90
b = 44.8	β = 90
c = 52.9	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
MERLOT	phasing
TNT	refinement
bioteX	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-10-14 
Deposition Author(s): Dung, M.H., Bell, J.A.

Revision History  

• Version 1.0: 1996-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary