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Yorodumi- PDB-7pvx: Crystal structure of the c-Src SH3 domain mutant E93V-S94A-R95S-T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pvx | ||||||
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Title | Crystal structure of the c-Src SH3 domain mutant E93V-S94A-R95S-T96G-N112G-N113Y-T114N-E115H in complex with the synthetic peptide VSL12 | ||||||
Components |
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Keywords | PROTEIN BINDING / beta barrel / SH3 domain | ||||||
Function / homology | non-specific protein-tyrosine kinase / Isoform 1 of Proto-oncogene tyrosine-protein kinase Src Function and homology information | ||||||
Biological species | Gallus gallus (chicken) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å | ||||||
Model details | Chimera construction c-Src-Abl SH3 domain | ||||||
Authors | Camara-Artigas, A. / Salinas Garcia, M.C. | ||||||
Funding support | Spain, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pvx.cif.gz | 91.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pvx.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 7pvx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pvx_validation.pdf.gz | 440 KB | Display | wwPDB validaton report |
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Full document | 7pvx_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 7pvx_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7pvx_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/7pvx ftp://data.pdbj.org/pub/pdb/validation_reports/pv/7pvx | HTTPS FTP |
-Related structure data
Related structure data | 4rtzS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | 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 | Mass: 1317.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 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
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.7749 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.41 Å2 / Biso mean: 26.7902 Å2 / Biso min: 13.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.43→24.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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