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.

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), 0.188 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80667
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53112
Sequence Annotations Expand
Reference Sequence

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), 0.188 (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

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Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Revision History (Full details and data files)

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

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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.