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.

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), 0.197 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YP5

This is version 1.4 of the entry. See complete history.

Literature

Yeast Myo5 SH3 domain, tetragonal crystal form

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04439
Sequence Annotations Expand
Reference Sequence

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), 0.197 (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

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Entry History

Deposition Data

Released Date: 2006-01-17

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.