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Yorodumi- PDB-1apl: CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1apl | ||||||
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Title | CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information : / regulation of mating-type specific transcription, DNA-templated / RNA polymerase II transcription repressor complex / DNA binding, bending / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Wolberger, C. / Vershon, A.K. / Liu, B. / Johnson, A.D. / Pabo, C.O. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1991 Title: Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Authors: Wolberger, C. / Vershon, A.K. / Liu, B. / Johnson, A.D. / Pabo, C.O. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Preliminary X-Ray Diffraction Studies of a MAT-Alpha2-DNA Complex Authors: Wolberger, C. / Vershon, A.K. / Johnson, A.D. / Pabo, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1apl.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1apl.ent.gz | 41.3 KB | Display | PDB format |
PDBx/mmJSON format | 1apl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1apl_validation.pdf.gz | 387.6 KB | Display | wwPDB validaton report |
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Full document | 1apl_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 1apl_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1apl_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1apl ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1apl | 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: DNA chain | Mass: 6381.160 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6501.232 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 9773.306 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MAT ALPHA2 RES. 128-210 / Plasmid: PAV56 / Gene (production host): MAT ALPHA2 RES. 128-210 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B2C0, UniProt: P0CY08*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.50, VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 217.11-13 1991 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.9 Å / Num. obs: 7334 / % possible obs: 90 % / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.65 Å / Num. obs: 7907 / Num. measured all: 18265 / Rmerge(I) obs: 0.075 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.7→8 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(I): 1 / Rfactor obs: 0.226 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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