2OQF | pdb_00002oqf

Structure of a synthetic, non-natural analogue of RNase A: [N71K(Ade), D83A]RNase A

• PDB DOI: https://doi.org/10.2210/pdb2OQF/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): Yes 


• Deposited: 2007-01-31 Released: 2008-02-12 
• Deposition Author(s): Boerema, D.J., Tereshko, V.A., Zhang, J.L., He, C., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.291 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Design, Synthesis, and Characterization of Non-natural RNase A Analogues with Enhanced Second-step Catalytic Activity

Boerema, D.J., Tereshko, V.A., Zhang, J.L., He, C., Kent, S.B.H.

To be published.

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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.19 kDa 
• Atom Count: 3,919 
• Modeled Residue Count: 494 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A, B, C, D	124	N/A	Mutation(s): 2  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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
XX1	A, B, C, D	L-PEPTIDE LINKING	C11 H16 N6 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.291 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.578	α = 85.26
b = 50.534	β = 74.31
c = 62.863	γ = 82.7

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Boerema, D.J., Tereshko, V.A., Zhang, J.L., He, C., Kent, S.B.H.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary