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- PDB-3jvt: Calcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with R... -
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Open data
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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 | ||||||
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![]() | 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 | ![]() cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril ...cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril / sarcomere organization / myosin heavy chain binding / mitotic cytokinesis / post-embryonic development / muscle contraction / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Himmel, D.M. / Mui, S. / O'Neall-Hennessey, E. / Szent-Gyorgyi, A. / Cohen, C. | ||||||
![]() | ![]() 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: ![]() Title: Structure of the Regulatory Domain of Scallop Myosin at 2 A Resolution: Implications for Regulation. Authors: Houdusse, A. / Cohen, C. #2: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.1 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.5 KB | Display | ![]() |
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Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jtdC ![]() 1wdcS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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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) ![]() |
#3: Protein | Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Bay Scallop / Source: (natural) ![]() |
-Non-polymers , 3 types, 249 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
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#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-CA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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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