[English] 日本語
Yorodumi
- PDB-7pvx: Crystal structure of the c-Src SH3 domain mutant E93V-S94A-R95S-T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pvx
TitleCrystal structure of the c-Src SH3 domain mutant E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H in complex with the synthetic peptide VSL12
Components
  • Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
  • VSL12 peptide
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homologynon-specific protein-tyrosine kinase / Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
Function and homology information
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
Model detailsChimera construction c-Src-Abl SH3 domain
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2006-78020-R Spain
CitationJournal: To be published
Title: Crystal structure of the c-Src SH3 domain mutants of the specificity region in complex with polyproline peptides
Authors: Camara-Artigas, A. / Salinas Garcia, M.C.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
B: VSL12 peptide
C: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
D: VSL12 peptide


Theoretical massNumber of molelcules
Total (without water)15,8424
Polymers15,8424
Non-polymers00
Water1,820101
1
A: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
B: VSL12 peptide


Theoretical massNumber of molelcules
Total (without water)7,9212
Polymers7,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area4370 Å2
MethodPISA
2
C: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
D: VSL12 peptide


Theoretical massNumber of molelcules
Total (without water)7,9212
Polymers7,9212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area4140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.991, 59.658, 37.349
Angle α, β, γ (deg.)90.000, 98.620, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Isoform 1 of Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 6603.213 Da / Num. of mol.: 2 / Mutation: E93V, S94A, R95S,T96G, N112G, N113Y, T114N, E115H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523-1, non-specific protein-tyrosine kinase
#2: Protein/peptide VSL12 peptide


Mass: 1317.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.98 % / Mosaicity: 0.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.0 M ammonium sulfate, 40 mM LiCl, 5% PEG 300, 10% glicerol, 0.1M MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.43→31.4 Å / Num. obs: 22814 / % possible obs: 98.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.055 / Net I/σ(I): 11.6 / Num. measured all: 72066 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.463.30.429372911440.9030.2810.5152.299.9
7.85-31.42.80.0353981430.9960.0240.0432992.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RTZ

4rtz


Resolution: 1.43→24.49 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1156 5.07 %
Rwork0.1737 21629 -
obs0.1756 22785 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.41 Å2 / Biso mean: 26.7902 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 1.43→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 0 101 1178
Biso mean---35.79 -
Num. residues----139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.50.29021560.22332706286299
1.5-1.580.30841390.211227142853100
1.58-1.680.25331450.178727292874100
1.68-1.810.2431360.1662738287499
1.81-1.990.21531580.16112686284499
1.99-2.280.18731530.15162679283298
2.28-2.870.20341260.18432694282097
2.87-24.490.1981430.17312683282696

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more