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Yorodumi- PDB-1mg4: STRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: WILD TYPE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mg4 | ||||||
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Title | STRUCTURE OF N-TERMINAL DOUBLECORTIN DOMAIN FROM DCLK: WILD TYPE PROTEIN | ||||||
Components | DOUBLECORTIN-LIKE KINASE (N-TERMINAL DOMAIN) | ||||||
Keywords | TRANSFERASE / DCX Domain / Doublecortin-like Kinase / Microtubule Bundling / Cortex Development | ||||||
Function / homology | Function and homology information central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration / response to virus / nervous system development / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.504 Å | ||||||
Authors | Kim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: The DCX-domain Tandems of Doublecortin and Doublecortin-like Kinase Authors: Kim, M.H. / Cierpickil, T. / Derewenda, U. / Krowarsch, D. / Feng, Y. / Devedjiev, Y. / Dauter, Z. / Walsh, C.A. / Otlewski, J. / Bushweller, J.H. / Derewenda, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mg4.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mg4.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/1mg4 ftp://data.pdbj.org/pub/pdb/validation_reports/mg/1mg4 | HTTPS FTP |
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-Related structure data
Related structure data | 1mfwSC 1mjdC 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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Unit cell |
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Details | BIOLOGICAL ASSEMBLY IS A TANDEM OF N-TERMINAL AND C-TERMINAL DOMAINS |
-Components
#1: Protein | Mass: 12877.623 Da / Num. of mol.: 1 / Fragment: (N-Terminal Domain), Residues 49-154 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O15075 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.4 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: CITRATE BUFFER, AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||
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: APS / Beamline: 19-ID / Wavelength: 0.9187 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2002 / Details: Double crystal focusing mirrors |
Radiation | Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9187 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 15460 / Num. obs: 15460 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 13.7 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1368 / % possible all: 85.7 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 50 Å / Num. measured all: 47701 |
Reflection shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.55 Å / % possible obs: 85.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MFW Resolution: 1.504→19.28 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.745 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.095 / ESU R Free: 0.074 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.754 Å2
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Refinement step | Cycle: LAST / Resolution: 1.504→19.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.504→1.543 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.153 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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