1KM9 | pdb_00001km9

The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog)

• PDB DOI: https://doi.org/10.2210/pdb1KM9/pdb

• Classification: HYDROLASE
• Organism(s): Aquarana catesbeiana
• Mutation(s): No 


• Deposited: 2001-12-14 Released: 2003-09-09 
• Deposition Author(s): Chern, S.-S., Musayev, F.N., Amiraslanov, I.R., Liao, Y.-D., Liaw, Y.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The Structure of a Cytotoxic Ribonuclease From the Oocyte of Rana Catesbeiana (Bullfrog)

Chern, S.-S., Musayev, F.N., Amiraslanov, I.R., Liao, Y.-D., Liaw, Y.-C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.74 kDa 
• Atom Count: 987 
• Modeled Residue Count: 111 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE, OOCYTES	A	111	Aquarana catesbeiana	Mutation(s): 0  EC: 3.1.27.5 (PDB Primary Data), 3.1.27 (UniProt)
UniProt
Find proteins for P11916 (Aquarana catesbeiana) Explore P11916  Go to UniProtKB:  P11916

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.806	α = 90
b = 45.918	β = 90
c = 57.459	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Chern, S.-S., Musayev, F.N., Amiraslanov, I.R., Liao, Y.-D., Liaw, Y.-C.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary