5OAV | pdb_00005oav

High resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with the high affinity synthetic peptide APP12: monoclinic crystal

PDB DOI: https://doi.org/10.2210/pdb5OAV/pdb

Classification: TRANSFERASE
Organism(s): Gallus gallus, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-06-23 Released: 2017-07-12
Deposition Author(s): Camara-Artigas, A.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free:
0.160 (Depositor), 0.158 (DCC)
R-Value Work:
0.141 (Depositor), 0.142 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

High resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with the high affinity synthetic peptide APP12: monoclinic crystal

Camara-Artigas, A.

To be published.

Macromolecule Content

Total Structure Weight: 16.63 kDa
Atom Count: 1,243
Modeled Residue Count: 134
Deposited Residue Count: 148
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A, C	61	Gallus gallus	Mutation(s): 1 Gene Names: SRC EC: 2.7.10.2
UniProt
Find proteins for P00523 (Gallus gallus) Explore P00523 Go to UniProtKB: P00523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00523
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
APP12	B, D	13	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.95 Å
R-Value Free: 0.160 (Depositor), 0.158 (DCC)
R-Value Work: 0.141 (Depositor), 0.142 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.804	α = 90
b = 31.801	β = 127.83
c = 61.634	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-07-12

Deposition Author(s):

Camara-Artigas, A.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BIO2016-78020-R

Revision History (Full details and data files)

Version 1.0: 2017-07-12
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence
Version 1.2: 2019-02-20
Changes: Data collection, Source and taxonomy
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-13
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.