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Yorodumi- PDB-1mij: Crystal Structure of the Homeo-prospero Domain of D. melanogaster... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mij | ||||||
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Title | Crystal Structure of the Homeo-prospero Domain of D. melanogaster Prospero | ||||||
Components | Protein prospero | ||||||
Keywords | TRANSCRIPTION / homeodomain / DNA-binding domain / prospero domain / 4-helix bundle | ||||||
Function / homology | Function and homology information regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / basal cortex / male courtship behavior / regulation of neuroblast proliferation / asymmetric neuroblast division ...regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / basal cortex / male courtship behavior / regulation of neuroblast proliferation / asymmetric neuroblast division / negative regulation of axonogenesis / neuroblast differentiation / axonogenesis involved in innervation / glial cell differentiation / apical cortex / peripheral nervous system development / regulation of protein localization to nucleus / regulation of DNA-binding transcription factor activity / dendrite morphogenesis / regulation of neuron differentiation / negative regulation of neuroblast proliferation / G1 to G0 transition / positive regulation of neuroblast proliferation / axon development / neuroblast proliferation / cell fate commitment / synapse assembly / axonogenesis / central nervous system development / axon guidance / protein localization / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sensory perception of taste / nervous system development / cell cortex / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Ryter, J.M. / Doe, C.Q. / Matthews, B.W. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of the DNA Binding Region of Prospero Reveals a Novel Homeo-Prospero Domain Authors: Ryter, J.M. / Doe, C.Q. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mij.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mij.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mij_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 1mij_full_validation.pdf.gz | 427.1 KB | Display | |
Data in XML | 1mij_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1mij_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/1mij ftp://data.pdbj.org/pub/pdb/validation_reports/mi/1mij | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18454.402 Da / Num. of mol.: 1 / Fragment: Homeo-prospero Domain (residues 1245-1396) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PROS / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29617 |
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#2: 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: 2.44 Å3/Da / Density % sol: 49.51 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 323 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris, n-tetradecyl beta-D-maltoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9790, 0.9793, 0.9611 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2001 | ||||||||||||
Radiation | Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→500 Å / Num. all: 11045 / Num. obs: 11045 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.05→500 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 500 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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