1R3M | pdb_00001r3m

Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease

• PDB DOI: https://doi.org/10.2210/pdb1R3M/pdb

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


• Deposited: 2003-10-02 Released: 2003-11-18 
• Deposition Author(s): Berisio, R., Sica, F., De Lorenzo, C., Di Fiore, A., Piccoli, R., Zagari, A., Mazzarella, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.292 (Depositor) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease

Berisio, R., Sica, F., De Lorenzo, C., Di Fiore, A., Piccoli, R., Zagari, A., Mazzarella, L.

(2003) FEBS Lett 554: 105-110

• PubMed: 14596923 
• DOI: https://doi.org/10.1016/s0014-5793(03)01114-1
• Primary Citation Related Structures: 
  1R3M


• PubMed Abstract: 
  

  Bovine seminal ribonuclease is a unique case of protein dimorphism, since it exists in two dimeric forms, with different biological and kinetic behavior, which interconvert into one another through three-dimensional swapping. Here we report the crystal structure, at 2.2 A resolution, of the unswapped form of bovine seminal ribonuclease. Besides completing the structural definition of bovine seminal ribonuclease conformational dimorphism, this study provides the structural basis to explain the dependence of the enzyme cooperative effects on its swapping state.

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 6, 80134 Naples, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 1,969 
• Modeled Residue Count: 244 
• Deposited Residue Count: 248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease, seminal	A, B	124	Bos taurus	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P00669 (Bos taurus) Explore P00669  Go to UniProtKB:  P00669

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.292 (Depositor) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.48	α = 90
b = 57.55	β = 116
c = 53.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-18 
Deposition Author(s): Berisio, R., Sica, F., De Lorenzo, C., Di Fiore, A., Piccoli, R., Zagari, A., Mazzarella, L.

Revision History  

• Version 1.0: 2003-11-18
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary