2Y9P | pdb_00002y9p

Pex4p-Pex22p mutant II structure

• PDB DOI: https://doi.org/10.2210/pdb2Y9P/pdb

• Classification: LIGASE/TRANSPORT PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-02-16 Released: 2012-02-29 
• Deposition Author(s): Williams, C., van den Berg, M., Panjikar, S., Distel, B., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 
  0.268 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Pex4P-Pex22P Structure

Williams, C., van den Berg, M., Panjikar, S., Distel, B., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 33.97 kDa 
• Atom Count: 2,204 
• Modeled Residue Count: 290 
• Deposited Residue Count: 302 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2-21 KDA	A	172	Saccharomyces cerevisiae	Mutation(s): 2  EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for P29340 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P29340  Go to UniProtKB:  P29340

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOME ASSEMBLY PROTEIN 22	B	130	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P39718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39718  Go to UniProtKB:  P39718

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free:  0.268 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.002	α = 90
b = 41.63	β = 98.46
c = 71.117	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Williams, C., van den Berg, M., Panjikar, S., Distel, B., Wilmanns, M.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description