+Open data
-Basic information
Entry | Database: PDB / ID: 2x51 | ||||||
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Title | M6 delta Insert1 | ||||||
Components |
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Keywords | MOTOR PROTEIN/SIGNALING PROTEIN / MOTOR PROTEIN-SIGNALING PROTEIN COMPLEX / ENDOCYTOSIS / PROTEIN TRANSPORT / CALMODULIN-BINDING / TRANSPORT / ACTIN-BINDING / GOLGI APPARATUS | ||||||
Function / homology | Function and homology information metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : ...metarhodopsin inactivation / myosin VI complex / myosin VI head/neck binding / myosin VII complex / photoreceptor cell axon guidance / negative regulation of opsin-mediated signaling pathway / rhabdomere / rhabdomere development / myosin V complex / : / regulation of secretion / kinetochore organization / : / actin filament-based movement / rhodopsin mediated signaling pathway / Neutrophil degranulation / inner ear auditory receptor cell differentiation / myosin V binding / channel regulator activity / vesicle transport along actin filament / cellular response to ethanol / myosin complex / clathrin-coated vesicle / microfilament motor activity / muscle cell cellular homeostasis / inner ear morphogenesis / myosin heavy chain binding / mitotic spindle pole / filamentous actin / microvillus / centriole replication / cytoskeletal motor activity / DNA damage response, signal transduction by p53 class mediator / enzyme regulator activity / ruffle / centriole / filopodium / actin filament organization / actin filament / ADP binding / sensory perception of sound / intracellular protein transport / mitotic spindle / spindle / ruffle membrane / endocytosis / actin filament binding / sensory perception of smell / actin cytoskeleton / cell cortex / midbody / cytoplasmic vesicle / nuclear membrane / vesicle / calmodulin binding / protein phosphorylation / centrosome / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SUS SCROFA (pig) DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Squires, G. / Houdusse, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Role of Insert-1 of Myosin Vi in Modulating Nucleotide Affinity. Authors: Pylypenko, O. / Song, L. / Squires, G. / Liu, X. / Zong, A.B. / Houdusse, A. / Sweeney, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x51.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x51.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x51 ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x51 | HTTPS FTP |
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-Related structure data
Related structure data | 2bkhS S: Starting model for refinement |
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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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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 90030.672 Da / Num. of mol.: 1 / Fragment: MYOSIN VI DELTA INSERT1,RESIDUES 1-277,303-817 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q29122 |
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#2: Protein | Mass: 16825.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P62152 |
-Non-polymers , 4 types, 262 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN A, ALA 303 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLY 548 TO VAL ...ENGINEERED |
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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: 1.84 Å3/Da / Density % sol: 33.37 % / Description: NONE |
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Crystal grow | pH: 6.75 Details: 10.8% PEG 8000, 50 MM MES PH 6.75, 175 MM AMMONIUM SULFATE, 3% ISO-PROPANOL, 3% TERT-BUTANOL, 4 MM EGTA. SOLUTION OF PROTEIN AT 18 MG/ML. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 60348 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.92 / Rsym value: 0.437 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BKH Resolution: 2.2→26.818 Å / SU ML: 0.28 / σ(F): 1.39 / Phase error: 28.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→26.818 Å
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Refine LS restraints |
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LS refinement shell |
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