+Open data
-Basic information
Entry | Database: PDB / ID: 1kk8 | ||||||
---|---|---|---|---|---|---|---|
Title | SCALLOP MYOSIN (S1-ADP-BeFx) IN THE ACTIN-DETACHED CONFORMATION | ||||||
Components |
| ||||||
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: 2.3 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. / HIMMEL, D. / SZENT-GYORGYI, A.G. / COHEN, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kk8.cif.gz | 234.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kk8.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 1kk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kk8 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kk8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1kk7C 1kqmC 1kwoC 1l2oC 1b7tS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 95543.750 Da / Num. of mol.: 1 / Fragment: MYOSIN HEAVY CHAIN / Mutation: FRAGMENT: PAPAIN DIGESTED, SUBFRAGMENT 1 (S1) / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P24733 |
---|---|
#2: Protein | Mass: 15888.021 Da / Num. of mol.: 1 / Fragment: MYOSIN REGULATORY LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P13543 |
#3: Protein | Mass: 17391.365 Da / Num. of mol.: 1 / Fragment: MYOSIN ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) Argopecten irradians (bay scallop) / Strain: BAY SCALLOP / References: UniProt: P07291 |
-Non-polymers , 6 types, 191 molecules
#4: Chemical | #5: Chemical | ChemComp-BEF / | #6: Chemical | ChemComp-ADP / | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-CA / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.76 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 20000, magnesium chloride, ethylene glycol, Tris HCl, ADP-berillium floride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / PH range low: 9 / PH range high: 8.5 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9298 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2000 / Details: mirrors |
Radiation | Monochromator: Rh-coated with Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9298 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 62330 / Num. obs: 49703 / % possible obs: 79.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 50.4 Å2 / Rsym value: 0.097 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4527 / Rsym value: 0.247 / % possible all: 72.7 |
Reflection | *PLUS Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS % possible obs: 72.7 % / Rmerge(I) obs: 0.247 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1B7T Resolution: 2.3→29.84 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 145691422.33 / Data cutoff high rms absF: 145691422.33 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.7641 Å2 / ksol: 0.335473 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.84 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor all: 0.234 / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.368 / Rfactor Rwork: 0.309 |