+Open data
-Basic information
Entry | Database: PDB / ID: 1dfl | ||||||
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Title | SCALLOP MYOSIN S1 COMPLEXED WITH MGADP:VANADATE-TRANSITION STATE | ||||||
Components | (MYOSIN HEAD) x 3 | ||||||
Keywords | CONTRACTILE PROTEIN / MYOSIN MOTOR / CONFORMATIONAL CHANGES | ||||||
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 / Resolution: 4.2 Å | ||||||
Authors | Houdusse, A. / Szent-Gyorgyi, A.G. / Cohen, C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Three conformational states of scallop myosin S1. Authors: Houdusse, A. / 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. #2: Journal: Structure / Year: 1996 Title: Structure of the Regulatory Domain of Scallop Myosin at 2 A Resolution: Implications for Regulation. Authors: Houdusse, A. / Cohen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dfl.cif.gz | 309.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dfl.ent.gz | 197.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dfl_validation.pdf.gz | 514.3 KB | Display | wwPDB validaton report |
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Full document | 1dfl_full_validation.pdf.gz | 549.6 KB | Display | |
Data in XML | 1dfl_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 1dfl_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1dfl ftp://data.pdbj.org/pub/pdb/validation_reports/df/1dfl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 6 molecules ABYWZX
#1: Protein | Mass: 94843.883 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P24733 #2: Protein | Mass: 15914.102 Da / Num. of mol.: 2 / Fragment: REGULATORY LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P13543 #3: Protein | Mass: 17165.070 Da / Num. of mol.: 2 / Fragment: ESSENTIAL LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / Tissue: SKELETAL MUSCLE / References: UniProt: P07291 |
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-Non-polymers , 4 types, 10 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Chemical | |
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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: 3.09 Å3/Da / Density % sol: 60.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 8000, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 4K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal amounts of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→40 Å / Num. obs: 426824 / % possible obs: 95.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 3.8→3.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.216 / % possible all: 80.9 |
Reflection | *PLUS Highest resolution: 3.8 Å / Lowest resolution: 40 Å / Num. obs: 29173 / Biso Wilson estimate: 30 Å2 / Num. measured all: 426824 |
Reflection shell | *PLUS % possible obs: 80.9 % |
-Processing
Software |
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Refinement | Resolution: 4.2→20 Å / σ(F): 1 Details: AT THIS RESOLUTION, WE PERFORMED ONLY A RIGID BODY REFINEMENT. NO POSITIONAL REFINEMENT WAS DONE.
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Refinement step | Cycle: LAST / Resolution: 4.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |