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Yorodumi- PDB-1l8r: Structure of the Retinal Determination Protein Dachshund Reveals ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1l8r | ||||||
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Title | Structure of the Retinal Determination Protein Dachshund Reveals a DNA-Binding Motif | ||||||
Components | Dachshund | ||||||
Keywords | TRANSCRIPTION / winged-helix | ||||||
Function / homology | Function and homology information development of primary female sexual characteristics / negative regulation of cell proliferation involved in contact inhibition / regulation of nuclear cell cycle DNA replication / respiratory gaseous exchange by respiratory system / negative regulation of transcription by competitive promoter binding / negative regulation of DNA biosynthetic process / suckling behavior / negative regulation of fibroblast proliferation / negative regulation of cell migration / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...development of primary female sexual characteristics / negative regulation of cell proliferation involved in contact inhibition / regulation of nuclear cell cycle DNA replication / respiratory gaseous exchange by respiratory system / negative regulation of transcription by competitive promoter binding / negative regulation of DNA biosynthetic process / suckling behavior / negative regulation of fibroblast proliferation / negative regulation of cell migration / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell population proliferation / transcription regulator complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Kim, S.S. / Zhang, R. / Braunstein, S.E. / Joachimiak, A. / Cvekl, A. / Hegde, R.S. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structure of the retinal determination protein Dachshund reveals a DNA binding motif. Authors: Kim, S.S. / Zhang, R.G. / Braunstein, S.E. / Joachimiak, A. / Cvekl, A. / Hegde, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l8r.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l8r.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 1l8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/1l8r ftp://data.pdbj.org/pub/pdb/validation_reports/l8/1l8r | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 11285.039 Da / Num. of mol.: 2 / Fragment: DACHbox-N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI36 #2: 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: 2.67 Å3/Da / Density % sol: 53.88 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: PEG 10000, Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, temperature 277K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: 0.97981, 0.97904, 0.95366 | ||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: May 1, 2001 | ||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.65→25.14 Å / Num. all: 56014 / Num. obs: 53166 / % possible obs: 96.5 % / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / % possible all: 91.5 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 26123 / Num. measured all: 227661 / Rmerge(I) obs: 0.064 | ||||||||||||
Reflection shell | *PLUS % possible obs: 91.5 % / Rmerge(I) obs: 0.233 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 6 Å / % reflection Rfree: 9 % / Rfactor obs: 0.237 / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.365 / Rfactor Rwork: 0.318 |