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Open data
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Basic information
Entry | Database: PDB / ID: 1kk7 | ||||||
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Title | SCALLOP MYOSIN IN THE NEAR RIGOR CONFORMATION | ||||||
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![]() | CONTRACTILE PROTEIN / Near rigor / Myosin / Mechanics of MOTOR / nucleotide free | ||||||
Function / homology | ![]() cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril ...cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril / sarcomere organization / myosin heavy chain binding / mitotic cytokinesis / post-embryonic development / muscle contraction / actin filament binding / calmodulin binding / calcium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Himmel, D.M. / Gourinath, S. / Reshetnikova, L. / Shen, Y. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
![]() | ![]() 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: ![]() Title: THREE CONFORMATIONAL STATES OF SCALLOP S1 Authors: HOUDUSSE, A. / SZENT-GYORGYI, A.G. / COHEN, C. #2: ![]() Title: ATOMIC STRUCTURE OFSCALLOP 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.3 KB | Display | ![]() |
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Full document | ![]() | 547.2 KB | Display | |
Data in XML | ![]() | 48.7 KB | Display | |
Data in CIF | ![]() | 65.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kk8C ![]() 1kqmC ![]() 1kwoC ![]() 1l2oC ![]() 1dfkS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules AYZ
#1: Protein | Mass: 95543.750 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) ![]() |
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#2: Protein | Mass: 17560.855 Da / Num. of mol.: 1 / Fragment: REGULATORY LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) ![]() |
#3: Protein | Mass: 17635.635 Da / Num. of mol.: 1 / Fragment: ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Details: PAPAIN DIGESTION OF MYOSIN / Source: (natural) ![]() |
-Non-polymers , 4 types, 14 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SO4 / | ||||
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#5: Chemical | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 62 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: PEG 5000, ammonium sulphate, MgCl2, gycerol, cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4.0 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2000 |
Radiation | Monochromator: Rh coated with Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 22975 / Num. obs: 20489 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 61.3 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1482 / Rsym value: 0.335 / % possible all: 65.8 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 20298 / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS % possible obs: 65.8 % / Rmerge(I) obs: 0.335 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DFK Resolution: 3.2→48.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2184630.18 / Data cutoff high rms absF: 2184630.18 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 161.96 Å2 / ksol: 0.312598 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→48.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor all: 0.263 / Rfactor Rfree: 0.313 / Rfactor Rwork: 0.258 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / Rfactor Rwork: 0.271 |