2OBY | pdb_00002oby

Crystal structure of Human P53 inducible oxidoreductase (TP53I3,PIG3)

• PDB DOI: https://doi.org/10.2210/pdb2OBY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-12-20 Released: 2007-01-30 
• Deposition Author(s): Porte, S., Valencia, E., Farres, J., Fita, I., Pike, A.C.W., Shafqat, N., Debreczeni, J., Johansson, C., Haroniti, A., Gileadi, O., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., von Delft, F., Oppermann, U., Pares, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human P53 inducible oxidoreductase (TP53I3, PIG3)

Porte, S., Valencia, E., Farres, J., Fita, I., Pike, A.C.W., Shafqat, N., Debreczeni, J., Johansson, C., Haroniti, A., Gileadi, O., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., von Delft, F., Oppermann, U., Pares, X.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 184.12 kDa 
• Atom Count: 12,823 
• Modeled Residue Count: 1,670 
• Deposited Residue Count: 1,690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative quinone oxidoreductase	A, B, C, D, E	338	Homo sapiens	Mutation(s): 0  Gene Names: TP53I3, PIG3 EC: 1 (PDB Primary Data), 1.6.5.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q53FA7 (Homo sapiens) Explore Q53FA7  Go to UniProtKB:  Q53FA7
PHAROS:  Q53FA7 GTEx:  ENSG00000115129

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.354	α = 90
b = 184.359	β = 90
c = 318.047	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Porte, S., Valencia, E., Farres, J., Fita, I., Pike, A.C.W., Shafqat, N., Debreczeni, J., Johansson, C., Haroniti, A., Gileadi, O., Arrowsmith, C.H., Edwards, A., Weigelt, J., Sundstrom, M., von Delft, F., Oppermann, U., Pares, X.

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description