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Yorodumi- PDB-2otg: Rigor-like structures of muscle myosins reveal key mechanical ele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2otg | ||||||
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Title | Rigor-like structures of muscle myosins reveal key mechanical elements in the transduction pathways of this allosteric motor | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / Myosin S1 / motor / rigor-like | ||||||
Function / homology | Function and homology information cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / locomotion / sarcomere organization / microfilament motor activity ...cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / locomotion / sarcomere organization / microfilament motor activity / myofibril / myosin heavy chain binding / mitotic cytokinesis / muscle contraction / post-embryonic development / actin filament binding / calcium ion binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Placopecten magellanicus (sea scallop) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||
Authors | Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Rigor-like Structures from Muscle Myosins Reveal Key Mechanical Elements in the Transduction Pathways of This Allosteric Motor. Authors: Yang, Y. / Gourinath, S. / Kovacs, M. / Nyitray, L. / Reutzel, R. / Himmel, D.M. / O'Neall-Hennessey, E. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Brown, J.H. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2otg.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2otg.ent.gz | 183.4 KB | Display | PDB format |
PDBx/mmJSON format | 2otg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2otg_validation.pdf.gz | 883.6 KB | Display | wwPDB validaton report |
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Full document | 2otg_full_validation.pdf.gz | 951.6 KB | Display | |
Data in XML | 2otg_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 2otg_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/2otg ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2otg | HTTPS FTP |
-Related structure data
Related structure data | 2ec6C 2os8C 3i5fC 3i5gC 3i5hC 3i5iC 1sr6S 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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Details | Myosin S1 in each assymmetric unit is a biological and biochemically active. |
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 96139.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26080 |
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#2: Protein | Mass: 17769.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26068 |
#3: Protein | Mass: 17811.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26066 |
-Non-polymers , 3 types, 4 molecules
#4: Chemical | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-CA / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG 2K, 5mM MgCl2, 100mM SrCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. all: 22033 / Num. obs: 22033 / % possible obs: 87.3 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 9.8 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.98 / Num. unique all: 956 / Rsym value: 36.8 / % possible all: 38.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SR6 Resolution: 3.12→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 201053.188 / 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: 10 Å2 / ksol: 0.239 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.12→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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