+Open data
-Basic information
Entry | Database: PDB / ID: 1sr6 | ||||||
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Title | Structure of nucleotide-free scallop myosin S1 | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / scallop myosin S1 / near rigor / complex salt bridge / novel conformation of nucleotide | ||||||
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 / Resolution: 2.75 Å | ||||||
Authors | Risal, D. / Gourinath, S. / Himmel, D.M. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 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: Journal: Structure / Year: 2003 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: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sr6.cif.gz | 233.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sr6.ent.gz | 184.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/1sr6 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/1sr6 | HTTPS FTP |
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-Related structure data
Related structure data | 1s5gC 1kk7S 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: 95815.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / 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 / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291 |
-Non-polymers , 4 types, 98 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |