3U00

Crystal structure of wild-type onconase at 1.65 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3U00/pdb

• Classification: HYDROLASE, ANTITUMOR PROTEIN
• Organism(s): Lithobates pipiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-28 Released: 2011-12-21 
• Deposition Author(s): Kurpiewska, K., Torrent, G., Ribo, M., Vilanova, M., Loch, J., Lewinski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of wild-type onconase at 1.65 A resolution

Kurpiewska, K., Torrent, G., Ribo, M., Vilanova, M., Loch, J., Lewinski, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.32 kDa 
• Atom Count: 996 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein P-30	A	104	Lithobates pipiens	Mutation(s): 0  EC: 3.1.27
UniProt
Find proteins for P22069 (Lithobates pipiens) Explore P22069  Go to UniProtKB:  P22069

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [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: 1.65 Å
• R-Value Free:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.509	α = 90
b = 39.454	β = 90
c = 69.985	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data collection
CrysalisPro	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Kurpiewska, K., Torrent, G., Ribo, M., Vilanova, M., Loch, J., Lewinski, K.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 2.0: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description
• Version 2.1: 2024-11-06
  Changes: Structure summary