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Yorodumi- PDB-5w1a: The first X-ray crystal structure of an insect muscle myosin. Dro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w1a | |||||||||
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Title | The first X-ray crystal structure of an insect muscle myosin. Drosophila melanogaster, skeletal muscle myosin II, an embryonic isoform, subfragment-1 | |||||||||
Components |
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Keywords | MOTOR PROTEIN / skeletal muscle myosin II / embryonic isoform / subfragment-1 / indirect flight muscle / insect | |||||||||
Function / homology | Function and homology information myosin filament organization / flight / RHO GTPases activate PAKs / adult somatic muscle development / muscle thin filament assembly / regulation of myosin II filament assembly / polytene chromosome puff / epithelial cell migration, open tracheal system / striated muscle myosin thick filament / border follicle cell migration ...myosin filament organization / flight / RHO GTPases activate PAKs / adult somatic muscle development / muscle thin filament assembly / regulation of myosin II filament assembly / polytene chromosome puff / epithelial cell migration, open tracheal system / striated muscle myosin thick filament / border follicle cell migration / myofibril assembly / muscle cell differentiation / skeletal muscle myosin thick filament assembly / muscle myosin complex / regulation of catalytic activity / locomotion / myosin complex / A band / muscle organ development / structural constituent of muscle / sarcomere organization / microfilament motor activity / myosin heavy chain binding / mesoderm development / enzyme regulator activity / sarcomere / muscle contraction / actin filament binding / protein stabilization / calmodulin binding / calcium ion binding / protein homodimerization activity / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.227 Å | |||||||||
Authors | Caldwell, J.T. / Bernstein, S.I. / Huxford, T. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: X-ray crystallographic and molecular dynamic analyses of Drosophila melanogaster embryonic muscle myosin define domains responsible for isoform-specific properties. Authors: Caldwell, J.T. / Mermelstein, D.J. / Walker, R.C. / Bernstein, S.I. / Huxford, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w1a.cif.gz | 717.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w1a.ent.gz | 598.2 KB | Display | PDB format |
PDBx/mmJSON format | 5w1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w1a ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w1a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 , 2 types, 4 molecules ACBD
#1: Protein | Mass: 91851.023 Da / Num. of mol.: 2 / Fragment: residues 1-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Tissue: indirect flight muscle / Gene: Mhc, CG17927 / Production host: Drosophila melanogaster (fruit fly) / Tissue (production host): indirect flight muscle / References: UniProt: P05661 #2: Protein | Mass: 17551.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Tissue: indirect flight muscle / Gene: Mlc1, MLC-ALK, CG5596 / Production host: Drosophila melanogaster (fruit fly) / Tissue (production host): indirect flight muscle / References: UniProt: P06742 |
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-Non-polymers , 4 types, 1073 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: 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: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 81% (0.1 M (0.03 M Citric acid, 0.07 BIS-TRIS propane, pH 7.1), 22% w/v PEG 3350), 9% Hampton Research Slice pH screen condition F9 (1.0 M TRIS hydrochloride, pH 8.1), and 10% Hampton ...Details: 81% (0.1 M (0.03 M Citric acid, 0.07 BIS-TRIS propane, pH 7.1), 22% w/v PEG 3350), 9% Hampton Research Slice pH screen condition F9 (1.0 M TRIS hydrochloride, pH 8.1), and 10% Hampton Research Silver Bullet Bio screen condition E11 (0.2% w/v 1,2-Diaminocyclohexane sulfate, 0.2% w/v Diloxanide furoate, 0.2% w/v Fumaric acid, 0.2% w/v Spermine, 0.2% w/v Sulfaguanidine, 0.02 M HEPES sodium pH 6.8) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.227→148.73 Å / Num. obs: 116714 / % possible obs: 99 % / Redundancy: 4.48 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.116 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.23→2.31 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.454 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.227→105.117 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.227→105.117 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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