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Open data
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Basic information
Entry | Database: PDB / ID: 1sr6 | ||||||
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Title | Structure of nucleotide-free scallop myosin S1 | ||||||
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![]() | CONTRACTILE PROTEIN / scallop myosin S1 / near rigor / complex salt bridge / novel conformation of nucleotide | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
![]() | ![]() Title: Myosin subfragment 1 structures reveal a partially bound nucleotide and a complex salt bridge that helps couple nucleotide and actin binding. Authors: Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C. #1: ![]() Title: Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head Authors: Gourinath, S. / Himmel, D.M. / Brown, J.H. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Cohen, C. #2: ![]() Title: Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor Authors: Himmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.9 KB | Display | ![]() |
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PDB format | ![]() | 184.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466 KB | Display | ![]() |
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Full document | ![]() | 530.3 KB | Display | |
Data in XML | ![]() | 46.7 KB | Display | |
Data in CIF | ![]() | 63.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s5gC ![]() 1kk7S 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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1 |
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 95815.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 4 types, 98 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / |
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#5: Chemical | ChemComp-MG / |
#6: Chemical | ChemComp-CA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 6% PEG 8000, 50mM ammonium sulfate, 8% glycerol, 10mM magnesium chloride, 50mM sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→38.79 Å / Num. all: 38495 / Num. obs: 31951 / % possible obs: 83 % / Observed criterion σ(F): -3 / Redundancy: 4 % / Biso Wilson estimate: 43.9 Å2 / Rsym value: 0.048 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.75→2.92 Å / Num. unique all: 3901 / Rsym value: 0.385 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1kk7 Resolution: 2.75→38.79 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 485766.54 / 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: 42.3919 Å2 / ksol: 0.338759 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→38.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |