1RNH

STRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb1RNH/pdb

• Classification: HYDROLASE(ENDORIBONUCLEASE)
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1990-07-11 Released: 1991-10-15 
• Deposition Author(s): Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein.

Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y.

(1990) Science 249: 1398-1405

• PubMed: 2169648 
• DOI: https://doi.org/10.1126/science.2169648
• Primary Citation of Related Structures:  
  1RNH


• PubMed Abstract: 
  

  Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.91 kDa 
• Atom Count: 1,300 
• Modelled Residue Count: 151 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE HI	A	155	Escherichia coli K-12	Mutation(s): 0  EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4  Go to UniProtKB:  P0A7Y4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 86.34	β = 90
c = 36.31	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-10-15 
Deposition Author(s): Yang, W., Hendrickson, W.A., Crouch, R.J., Satow, Y.

Revision History  

• Version 1.0: 1991-10-15
  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: 2024-06-05
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Structure summary