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Yorodumi- PDB-5jdj: Crystal structure of domain I10 from titin in space group P212121 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jdj | ||||||
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Title | Crystal structure of domain I10 from titin in space group P212121 | ||||||
Components | Titin | ||||||
Keywords | STRUCTURAL PROTEIN / titin / muscle | ||||||
Function / homology | Function and homology information sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy ...sarcomerogenesis / structural molecule activity conferring elasticity / telethonin binding / skeletal muscle myosin thick filament assembly / cardiac myofibril assembly / muscle alpha-actinin binding / detection of muscle stretch / cardiac muscle tissue morphogenesis / regulation of catalytic activity / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / M band / actinin binding / I band / cardiac muscle cell development / regulation of protein kinase activity / sarcomere organization / structural constituent of muscle / skeletal muscle thin filament assembly / striated muscle thin filament / striated muscle contraction / protein kinase A signaling / cardiac muscle contraction / muscle contraction / condensed nuclear chromosome / positive regulation of protein secretion / Z disc / response to calcium ion / : / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.738 Å | ||||||
Authors | Williams, R. / Bogomolovas, J. / Labiet, S. / Mayans, O. | ||||||
Citation | Journal: Open Biology / Year: 2016 Title: Exploration of pathomechanisms triggered by a single-nucleotide polymorphism in titin's I-band: the cardiomyopathy-linked mutation T2580I. Authors: Bogomolovas, J. / Fleming, J.R. / Anderson, B.R. / Williams, R. / Lange, S. / Simon, B. / Khan, M.M. / Rudolf, R. / Franke, B. / Bullard, B. / Rigden, D.J. / Granzier, H. / Labeit, S. / Mayans, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdj.cif.gz | 323.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdj.ent.gz | 262.8 KB | Display | PDB format |
PDBx/mmJSON format | 5jdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdj ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdj | HTTPS FTP |
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-Related structure data
-Links
-Assembly
-Components
#1: Protein | Mass: 10178.617 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTN / Production host: Escherichia coli (E. coli) References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase #2: Chemical | ChemComp-CA / #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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M CaCl2, 0.1 M Tris pH 7.5, 25% [w/v] PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.738→29.652 Å / Num. obs: 145378 / % possible obs: 98.77 % / Redundancy: 7.5 % / Rsym value: 0.096 / Net I/σ(I): 15.38 |
Reflection shell | Resolution: 1.738→1.8 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.77 / Num. unique all: 13857 / Rsym value: 0.714 / % possible all: 95.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.738→29.652 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.02 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.738→29.652 Å
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Refine LS restraints |
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LS refinement shell |
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