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Yorodumi- PDB-3lla: Crystal Structure of the Alpha-kinase Domain of Myosin Heavy Chai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lla | ||||||
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Title | Crystal Structure of the Alpha-kinase Domain of Myosin Heavy Chain Kinase A Complex with AMPPCP | ||||||
Components | Myosin heavy chain kinase A | ||||||
Keywords | TRANSFERASE / Protein kinase like fold / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / Alpha-kinase / Coiled coil / WD repeat | ||||||
Function / homology | Function and homology information myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis ...myosin-heavy-chain kinase / myosin heavy chain kinase activity / myosin II filament disassembly / ADP phosphatase activity / actomyosin contractile ring / actin crosslink formation / myosin II binding / AMP binding / actin filament bundle assembly / mitotic cytokinesis / cAMP binding / ADP binding / chemotaxis / actin filament binding / cell cortex / protein autophosphorylation / protein kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Ye, Q. / Jia, Z. | ||||||
Citation | Journal: Sci.Signal. / Year: 2010 Title: Crystal Structure of the {alpha}-Kinase Domain of Dictyostelium Myosin Heavy Chain Kinase A. Authors: Ye, Q. / Crawley, S.W. / Yang, Y. / Cote, G.P. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lla.cif.gz | 126.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lla.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3lla ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3lla | HTTPS FTP |
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-Related structure data
Related structure data | 3lkmSC 3lmhC 3lmiC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 34526.582 Da / Num. of mol.: 2 / Fragment: UNP residues 552-841 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Strain: AX3 / Gene: DDB_G0291231, mhckA, mhkA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42527, myosin-heavy-chain kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.63 Å3/Da / Density % sol: 53.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% PEG 8000, 0.2M sodium phosphate, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2007 / Details: Synchrotron optics |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→25 Å / Num. obs: 42537 / % possible obs: 99.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 37.69 |
Reflection shell | Resolution: 2.11→2.18 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.1 / Num. unique all: 4197 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LKM Resolution: 2.11→23.9 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.082 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.164 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→23.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.165 Å / Total num. of bins used: 20
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