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Yorodumi- PDB-3jvt: Calcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jvt | ||||||
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Title | Calcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with Reconstituted Complete Light Chains | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / Regulated myosins / smooth and molluscan muscle / X-ray crystallographic structure / scallop regulatory domain/lever arm / on-state / calcium-binding protein / Actin-binding / ATP-binding / Calmodulin-binding / Coiled coil / Cytoplasm / Motor protein / Muscle protein / Myosin / Nucleotide-binding / Thick filament / Calcium | ||||||
Function / homology | Function and homology information myosin filament / myosin complex / myofibril / cytoskeletal motor activity / actin filament binding / calmodulin binding / calcium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Argopecten irradians (bay scallop) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Himmel, D.M. / Mui, S. / O'Neall-Hennessey, E. / Szent-Gyorgyi, A. / Cohen, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: The on-off switch in regulated myosins: different triggers but related mechanisms. Authors: Himmel, D.M. / Mui, S. / O'Neall-Hennessey, E. / Szent-Gyorgyi, A.G. / Cohen, C. #1: Journal: Structure / Year: 1996 Title: Structure of the Regulatory Domain of Scallop Myosin at 2 A Resolution: Implications for Regulation. Authors: Houdusse, A. / Cohen, C. #2: Journal: Nature / Year: 1994 Title: Structure of the Regulatory Domain of Scallop Myosin at 2.8 A Resolution. Authors: Xie, X. / Harrison, D.H. / Schlichting, I. / Sweet, R.M. / Kalabokis, V.N. / Szent-Gyorgyi, A. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jvt.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jvt.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 3jvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/3jvt ftp://data.pdbj.org/pub/pdb/validation_reports/jv/3jvt | HTTPS FTP |
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-Related structure data
Related structure data | 3jtdC 1wdcS C: citing same article (ref.) 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 8128.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P24733 |
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#2: Protein | Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P13543 |
#3: Protein | Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291 |
-Non-polymers , 3 types, 249 molecules
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-CA / |
#6: 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: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 150 mM HEPES pH 7.0, 50 mM Ammonium Sulfate, 0.5 mM Calcium Chloride, 5 mM Magnesium Chloride, 5 mM Sodium Azide, 16.5% (wt/vol) PEG 4000 combined with equal volume of 16.9 mg/ml protein in ...Details: 150 mM HEPES pH 7.0, 50 mM Ammonium Sulfate, 0.5 mM Calcium Chloride, 5 mM Magnesium Chloride, 5 mM Sodium Azide, 16.5% (wt/vol) PEG 4000 combined with equal volume of 16.9 mg/ml protein in 5 mM HEPES pH 7, 20 mM NaCl, 2 mM Magnesium Chloride, 0.2 mM Calcium Chloride, 0.1 mM EGTA, 3.0 mM Sodium Azide, Hanging drop vapor diffusion, temperature 277K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 Å |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 26353 / Num. obs: 25062 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.8 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.047 / Net I/σ(I): 9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WDC Resolution: 2.1→9.99 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.856 / Data cutoff high absF: 160980 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.703 Å2 / ksol: 0.411 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.93 Å2 / Biso mean: 33.04 Å2 / Biso min: 8.91 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.22 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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