+Open data
-Basic information
Entry | Database: PDB / ID: 1kqm | ||||||
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Title | SCALLOP MYOSIN S1-AMPPNP IN THE ACTIN-DETACHED CONFORMATION | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN / actin-detached / Myosin / Mechanics of MOTOR | ||||||
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: 3 Å | ||||||
Authors | Himmel, D.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 | 1kqm.cif.gz | 226.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kqm.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kqm ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kqm | HTTPS FTP |
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-Related structure data
Related structure data | 1kk7C 1kk8C 1kwoC 1l2oC 1b7tS 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 peptide chains (heavy chain, regulatory light chain, essential light chain), which can 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: MUSCLESkeletal 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: MUSCLESkeletal 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: MUSCLESkeletal muscle / References: UniProt: P07291 |
-Non-polymers , 4 types, 11 molecules
#4: Chemical | #5: Chemical | ChemComp-ANP / | #6: Chemical | ChemComp-CA / | #7: 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: 3.43 Å3/Da / Density % sol: 64.1 % |
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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, AMPPNP, 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: 1.087 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 1999 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.087 Å / Relative weight: 1 |
Reflection | Resolution: 3→40 Å / Num. all: 34823 / Num. obs: 31019 / % possible obs: 80.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 39.8 Å2 / Rsym value: 0.077 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5.6 / Num. unique all: 1898 / Rsym value: 0.472 / % possible all: 53.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B7T Resolution: 3→39.81 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 243778.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 19.2434 Å2 / ksol: 0.251994 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→39.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.04 Å / Rfactor Rfree error: 0.1 / Total num. of bins used: 25
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Xplor file |
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