+Open data
-Basic information
Entry | Database: PDB / ID: 1l2o | ||||||
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Title | SCALLOP MYOSIN S1-ADP-p-PDM IN THE ACTIN-DETACHED CONFORMATION | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / actin-detached / Myosin / Mechanics of MOTOR / cross linker | ||||||
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 / calmodulin binding / calcium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Argopecten irradians (bay scallop) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Himmel, M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, G. / Cohen, C. | ||||||
Citation | 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. #1: Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Atomic Structure of Scallop Myosin Subfragment S1 Complexed with MgADP: A Novel Conformation of the Myosin Head Authors: Houdusse, A. / Kalabokis, V.N. / Himmel, D. / 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 | 1l2o.cif.gz | 226 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l2o.ent.gz | 172.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1l2o_validation.pdf.gz | 535.1 KB | Display | wwPDB validaton report |
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Full document | 1l2o_full_validation.pdf.gz | 626.1 KB | Display | |
Data in XML | 1l2o_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 1l2o_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/1l2o ftp://data.pdbj.org/pub/pdb/validation_reports/l2/1l2o | HTTPS FTP |
-Related structure data
Related structure data | 1kk7C 1kk8SC 1kqmC 1kwoC S: Starting model for refinement C: citing same article (ref.) |
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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 consists of three poly-peptide chains (heavy chain, regulatory light chain, essential light chain), and can thus also be described as a heterotrimer |
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 95317.430 Da / Num. of mol.: 1 / Fragment: SUBFRAGMENT 1(S1) / Source method: isolated from a natural source / Details: papain digested / Source: (natural) Argopecten irradians (bay scallop) / Tissue: muscle / 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) / Tissue: muscle / 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) / Tissue: muscle / References: UniProt: P07291 |
-Non-polymers , 5 types, 36 molecules
#4: Chemical | #5: Chemical | ChemComp-PDM / | #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-CA / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 20000, magnesium chloride, ethylene glycol, Tris HCl, ATPgammaS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 1999 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→55 Å / Num. all: 30488 / Num. obs: 29564 / % possible obs: 74.4 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 54.3 Å2 / Rsym value: 0.035 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.8→2.98 Å / Num. unique all: 1584 / Rsym value: 0.153 / % possible all: 24.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KK8 Resolution: 2.8→54.16 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 37648249.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent model used
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.736 Å2 / ksol: 0.29497 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→54.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
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Xplor file |
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