2A08 | pdb_00002a08

Structure of the yeast YHH6 SH3 domain

• PDB DOI: https://doi.org/10.2210/pdb2A08/pdb

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


• Deposited: 2005-06-16 Released: 2006-06-27 
• Deposition Author(s): Kursula, P., Kursula, I., Song, Y.H., Lehmann, F., Zou, P., Wilmanns, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

3-D proteome of yeast SH3 domains

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.03 kDa 
• Atom Count: 1,149 
• Modeled Residue Count: 116 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region	A, B	60	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32793  Go to UniProtKB:  P32793

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.215 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.83	α = 90
b = 66.83	β = 90
c = 52.68	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Kursula, P., Kursula, I., Song, Y.H., Lehmann, F., Zou, P., Wilmanns, M.

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description