4HAA | pdb_00004haa

Structure of Ribonuclease Binase Glu43Ala/Phe81Ala Mutant

• PDB DOI: https://doi.org/10.2210/pdb4HAA/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus intermedius
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-26 Released: 2012-10-17 
• Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Mitchevich, V.A., Dorovatovskii, P.V., Schulga, A.A., Makarov, A.A., Tkach, E.N., Goncharuk, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.205 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Structure and functional studies of the ribonuclease binase Glu43Ala/Phe81Ala mutant.

Mitkevich, V.A., Schulga, A.A., Trofimov, A.A., Dorovatovskii, P.V., Goncharuk, D.A., Tkach, E.N., Makarov, A.A., Polyakov, K.M.

(2013) Acta Crystallogr D Biol Crystallogr 69: 991-996

• PubMed: 23695243 
• DOI: https://doi.org/10.1107/S0907444913004046
• Primary Citation Related Structures: 
  4HAA


• PubMed Abstract: 
  

  Ribonuclease from Bacillus intermedius (binase) is a small basic protein with antitumour activity. The three-dimensional structure of the binase mutant form Glu43Ala/Phe81Ala was determined at 1.98 Å resolution and its functional properties, such as the kinetic parameters characterizing the hydrolysis of polyinosinic acid and cytotoxicity towards Kasumi-1 cells, were investigated. In all crystal structures of binase studied previously the characteristic dimer is present, with the active site of one subunit being blocked owing to interactions within the dimer. In contrast to this, the new mutant form is not dimeric in the crystal. The catalytic efficiency of the mutant form is increased 1.7-fold and its cytotoxic properties are enhanced compared with the wild-type enzyme.

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Organizational Affiliation: 
• Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.37 kDa 
• Atom Count: 3,688 
• Modeled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease	A, B, C, D	109	Bacillus intermedius	Mutation(s): 2  EC: 3.1.27
UniProt
Find proteins for P00649 (Bacillus intermedius) Explore P00649  Go to UniProtKB:  P00649

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.205 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.36	α = 90
b = 50.36	β = 90
c = 196.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Polyakov, K.M., Trofimov, A.A., Mitchevich, V.A., Dorovatovskii, P.V., Schulga, A.A., Makarov, A.A., Tkach, E.N., Goncharuk, D.A.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description