Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.56 kDa 
• Atom Count: 1338 
• Modelled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 1

1RBV

STRUCTURAL STUDY OF MUTANTS OF ESCHERICHIA COLI RIBONUCLEASE HI WITH ENHANCED THERMOSTABILITY

• PDB DOI: 10.2210/pdb1RBV/pdb

• Classification: HYDROLASE(ENDORIBONUCLEASE)
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-02-16 Released: 1994-01-31 
• Deposition Author(s): Ishikawa, K., Kimura, S., Kanaya, S., Morikawa, K., Nakamura, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.180 

Literature

Structural study of mutants of Escherichia coli ribonuclease HI with enhanced thermostability.

Ishikawa, K., Kimura, S., Kanaya, S., Morikawa, K., Nakamura, H.

(1993) Protein Eng 6: 85-91

• PubMed: 8381958 
• DOI: 10.1093/protein/6.1.85
• Primary Citation of Related Structures:  
  1RBR, 1RBS, 1RBT, 1RBU, 1RBV


• PubMed Abstract: 
  

Systematic replacement of the amino acid residues in Escherichia coli ribonuclease HI with those in the thermophilic counterpart has revealed that two mutations, His62-->Pro (H62P) and Lys95-->Gly (K95G), increased the thermostability of the protein. These single-site mutant proteins, together with the mutant proteins His62-->Ala (H62A), Lys95-->Asn (K95N) and Lys95-->Ala (K95A), were crystallized and their structures were determined at 1.8 A resolution. The crystal structures of these mutant proteins reveal that only the local structure around each mutation site is essential for the increase in thermostability. For each mutant protein, the stabilization mechanism is considered to be as follows: (i) H62P is stabilized because of a decrease in the entropy of the unfolded state, without a change in the native backbone structure; (ii) K95G is stabilized since the strain caused by the left-handed backbone structure in the typical 3:5 type loop is eliminated; and (iii) K95N is slightly stabilized by a hydrogen bond formed between the side-chain N delta-atom of the mutated aspargine residue and the main-chain carbonyl oxygen within the same residue.

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Related Citations: 

• Structural Details of Ribonuclease H from Escherichia Coli as Refined at an Atomic Resolution
  Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Nakamura, H., Ikehara, M., Matsuzaki, T., Morikawa, K.
  (1992) J Mol Biol 223: 1029

• Three-Dimensional Structure of Ribonuclease H from E. Coli
  Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Ikehara, M., Matsuzaki, T., Morikawa, K.
  (1990) Nature 347: 306

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Organizational Affiliation: 

Protein Engineering Research Institute, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE H	A	155	Escherichia coli	Mutation(s): 0  EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4  Go to UniProtKB:  P0A7Y4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.12	α = 90
b = 86.81	β = 90
c = 35.56	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-02-16 
• Released Date: 1994-01-31 
Deposition Author(s): Ishikawa, K., Kimura, S., Kanaya, S., Morikawa, K., Nakamura, H.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other