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Yorodumi- PDB-5wjb: Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wjb | ||||||
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Title | Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Gp7 | ||||||
Components | Capsid assembly scaffolding protein,Myosin-7 | ||||||
Keywords | Actin/DNA Binding Protein / Myosin / Gp7 / Coiled-Coil / Actin-DNA Binding Protein complex | ||||||
Function / homology | Function and homology information viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress ...viral scaffold / regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / muscle myosin complex / muscle filament sliding / transition between fast and slow fiber / regulation of the force of heart contraction / myosin filament / adult heart development / cardiac muscle hypertrophy in response to stress / myosin II complex / myosin complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / microfilament motor activity / myofibril / virion assembly / skeletal muscle contraction / striated muscle contraction / muscle contraction / cardiac muscle contraction / stress fiber / ATP metabolic process / regulation of heart rate / sarcomere / Z disc / actin filament binding / calmodulin binding / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.905 Å | ||||||
Authors | Andreas, M.P. / Ajay, G. / Gellings, J. / Rayment, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Struct. Biol. / Year: 2017 Title: Design considerations in coiled-coil fusion constructs for the structural determination of a problematic region of the human cardiac myosin rod. Authors: Andreas, M.P. / Ajay, G. / Gellings, J.A. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wjb.cif.gz | 201.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wjb.ent.gz | 161.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wjb_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 5wjb_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 5wjb_validation.xml.gz | 17 KB | Display | |
Data in CIF | 5wjb_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wjb ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wjb | HTTPS FTP |
-Related structure data
Related structure data | 5wj7C 5wlqC 5wlzC 5wmeC 1no4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15907.618 Da / Num. of mol.: 4 Fragment: UNP P13848 residues 2-47, UNP P12833 residues 1733-1797 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Homo sapiens (human) Gene: MYH7, MYHCB / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus / References: UniProt: P13848, UniProt: P12883 #2: 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: 2.4 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% (w/v) methyl-ether PEG 2K, 1.5%(w/v) myo-inositol, 100 mM HEPES pH 7.5, 50 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. obs: 13797 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 19.296 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 688 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NO4 Resolution: 2.905→49.638 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.905→49.638 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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