+Open data
-Basic information
Entry | Database: PDB / ID: 2y9r | ||||||
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Title | Crystal structure of the M10 domain of Titin | ||||||
Components | TITIN | ||||||
Keywords | TRANSFERASE / SARCOMERE / M-BAND / IMMUNOGLOBULIN DOMAIN | ||||||
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 / cardiac muscle hypertrophy / mitotic chromosome condensation ...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 / cardiac muscle hypertrophy / mitotic chromosome condensation / Striated Muscle Contraction / actinin binding / M band / I band / protein kinase regulator activity / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / skeletal muscle thin filament assembly / striated muscle thin filament / condensed nuclear chromosome / striated muscle contraction / muscle contraction / cardiac muscle contraction / protein kinase A signaling / positive regulation of protein secretion / response to calcium ion / Z disc / actin filament binding / Platelet degranulation / protein tyrosine kinase activity / protease binding / calmodulin binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / positive regulation of gene expression / protein kinase binding / enzyme binding / protein homodimerization activity / 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: 1.9 Å | ||||||
Authors | Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Titin M10 Domain Authors: Pernigo, S. / Fukuzawa, A. / Gautel, M. / Steiner, R.A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural Insight Into M-Band Assembly and Mechanics from the Titin-Obscurin-Like-1 Complex. Authors: Pernigo, S. / Fukuzawa, A. / Bertz, M. / Holt, M. / Rief, M. / Steiner, R.A. / Gautel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y9r.cif.gz | 57 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y9r.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y9r_validation.pdf.gz | 818.2 KB | Display | wwPDB validaton report |
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Full document | 2y9r_full_validation.pdf.gz | 819.6 KB | Display | |
Data in XML | 2y9r_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 2y9r_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/2y9r ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y9r | HTTPS FTP |
-Related structure data
Related structure data | 2wp3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10981.231 Da / Num. of mol.: 1 / Fragment: M10 DOMAIN, RESIDUES 26828-26926 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 References: UniProt: Q8WZ42, non-specific serine/threonine protein kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.32 % Description: CHAIN T OF 2WP3 WAS USED FOR MOLECULAR REPLACEMENT |
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Crystal grow | pH: 6.5 / Details: 35% PEG 400, 0.1M BIS-TRIS PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9704 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 4, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9704 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→34.42 Å / Num. obs: 8350 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WP3 Resolution: 1.9→34.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.802 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS AT RIDING POSITIONS HAVE BEEN USED IN REFINEMENT. N-TERMINAL GLY-SER-SER RESIDUES FROM THE VECTOR AND C-TERMINAL ILE ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.422 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.42 Å
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Refine LS restraints |
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