3PHN | pdb_00003phn

Crystal structure of wild-type onconase with resolution 1.46 A

• PDB DOI: https://doi.org/10.2210/pdb3PHN/pdb

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


• Deposited: 2010-11-04 Released: 2010-11-17 
• 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: 1.46 Å
• R-Value Free: 
  0.199 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Structure of Rana pipiens wild-type onconase at resolution 1.46 A

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: 12.19 kDa 
• Atom Count: 1,132 
• Modeled 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.46 Å
• R-Value Free:  0.199 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.23	α = 90
b = 38.679	β = 90
c = 69.588	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Kurpiewska, K., Torrent, G., Ribo, M., Vilanova, M., Loch, J., Lewinski, K.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-10-30
  Changes: Structure summary