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Yorodumi- PDB-3lmi: Crystal Structure of the Inactive Alpha-kinase Domain of Myosin H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lmi | ||||||
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Title | Crystal Structure of the Inactive Alpha-kinase Domain of Myosin Heavy Chain Kinase A (D766A) complex with ATP | ||||||
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: 2.2 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 | 3lmi.cif.gz | 230 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lmi.ent.gz | 181.1 KB | Display | PDB format |
PDBx/mmJSON format | 3lmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/3lmi ftp://data.pdbj.org/pub/pdb/validation_reports/lm/3lmi | HTTPS FTP |
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-Related structure data
Related structure data | 3lkmSC 3llaC 3lmhC 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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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34482.570 Da / Num. of mol.: 4 / Fragment: UNP residues 552-841 / Mutation: D766A 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 |
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-Non-polymers , 5 types, 589 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ATP / #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: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 0.2M potassium phosphate, 0.1M Tris-HCl, pH 7.5, 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: Apr 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 56572 / % possible obs: 92.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.63 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 6.723 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LKM Resolution: 2.2→29.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.869 / SU B: 5.701 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.249 / 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: 21.452 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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