1YP5 | pdb_00001yp5

Yeast Myo5 SH3 domain, tetragonal crystal form

• PDB DOI: https://doi.org/10.2210/pdb1YP5/pdb

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


• Deposited: 2005-01-29 Released: 2006-01-17 
• Deposition Author(s): Gonfloni, S., Kursula, P., Sacco, R., Cesareni, G., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Yeast Myo5 SH3 domain, tetragonal crystal form

Gonfloni, S., Kursula, P., Sacco, R., Cesareni, G., Wilmanns, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.38 kDa 
• Atom Count: 526 
• Modeled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin-5 isoform	A	58	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q04439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04439  Go to UniProtKB:  Q04439

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.62	α = 90
b = 34.62	β = 90
c = 99.48	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Gonfloni, S., Kursula, P., Sacco, R., Cesareni, G., Wilmanns, M.

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-09-26
  Changes: Data collection, Database references, Structure summary
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references