1RBJ | pdb_00001rbj

RIBONUCLEASE B COMPLEX WITH D(TETRA-(DEOXY-ADENYLATE))

• PDB DOI: https://doi.org/10.2210/pdb1RBJ/pdb
• NAKB: 1RBJ

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


• Deposited: 1995-05-22 Released: 1995-12-07 
• Deposition Author(s): Ko, T.-P., Williams, R., McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Structure of a ribonuclease B+d(pA)4 complex.

Ko, T.P., Williams, R., McPherson, A.

(1996) Acta Crystallogr D Biol Crystallogr 52: 160-164

• PubMed: 15299737 
• DOI: https://doi.org/10.1107/S0907444995009127
• Primary Citation Related Structures: 
  1RBJ


• PubMed Abstract: 
  

  The structure of a tetragonal crystal of bovine pancreatic RNase B complexed with d(pA)(4) was determined by molecular replacement and difference Fourier methods. This crystal belongs to space group P4(1)2(1)2 and has unit-cell dimensions a = b = 44.5, c = 156.5 A. The model consists of the enzyme and a tetranucleotide with fractional occupancies, suggesting multiple modes of oligonucleotide binding. It does not include any polysaccharide residues or solvent molecules. After refinement at 2.7 A, the R value was 0.163 with acceptable stereochemistry. The model illustrates a set of well defined interactions for substrate binding, particularly between the central dinucleotide and the enzyme.

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Organizational Affiliation: 
• Department of Biochemistry, University of California, Riverside 92521, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.92 kDa 
• Atom Count: 1,035 
• Modeled Residue Count: 128 
• Deposited Residue Count: 128 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RIBONUCLEASE B (E.C.3.1.27.5))	B [auth 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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*A)-3')	A [auth B]	4	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.45	α = 90
b = 44.45	β = 90
c = 156.5	γ = 90

Software Package:

Software Name	Purpose
ORESTES	data collection
TNT	refinement
ORESTES	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-12-07 
Deposition Author(s): Ko, T.-P., Williams, R., McPherson, A.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Structure summary