2V1R | pdb_00002v1r

Yeast Pex13 SH3 domain complexed with a peptide from Pex14 at 2.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2V1R/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-29 Released: 2008-06-03 
• Deposition Author(s): Kursula, I., Kursula, P., Lehmann, F., Zou, P., Song, Y.H., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Structural Genomics of Yeast SH3 Domains

Kursula, P., Kursula, I., Pinotsis, N., Lehmann, F., Zou, P., Song, Y.H., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.8 kDa 
• Atom Count: 1,369 
• Modeled Residue Count: 158 
• Deposited Residue Count: 205 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOMAL MEMBRANE PROTEIN PAS20	A, B	80	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P80667 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P80667  Go to UniProtKB:  P80667

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEX14	C [auth P], D [auth Q], E [auth R]	15	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53112  Go to UniProtKB:  P53112

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.44	α = 86.85
b = 39.09	β = 65.46
c = 39.14	γ = 62.04

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Kursula, I., Kursula, P., Lehmann, F., Zou, P., Song, Y.H., Wilmanns, M.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2013-08-07
  Changes: Derived calculations, Other, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary