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Yorodumi- PDB-1le8: Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1le8 | ||||||
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Title | Crystal Structure of the MATa1/MATalpha2-3A Heterodimer Bound to DNA Complex | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / MATalpha2 / isothermal titration calorimetry / protein-DNA complex / TRANSCRIPTION-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 / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ke, A. / Mathias, J.R. / Vershon, A.K. / Wolberger, C. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural and Thermodynamic Characterization of the DNA Binding Properties of a Triple Alanine Mutant of MATalpha2 Authors: Ke, A. / Mathias, J.R. / Vershon, A.K. / Wolberger, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1le8.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1le8.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 1le8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1le8_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 1le8_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 1le8_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1le8_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1le8 ftp://data.pdbj.org/pub/pdb/validation_reports/le/1le8 | HTTPS FTP |
-Related structure data
Related structure data | |
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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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-Components
#1: DNA chain | Mass: 6109.019 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6153.011 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 6277.417 Da / Num. of mol.: 1 / Fragment: residues 74-126 / Source method: obtained synthetically Details: The peptide was chemically synthesized with solid phase peptide synthesizer. The sequence of the peptide is naturally found in Saccharomyces cerevisiae (yeast). References: UniProt: P01366, UniProt: P0CY10*PLUS |
#4: Protein | Mass: 9628.164 Da / Num. of mol.: 1 / Fragment: residues 128-210 / Mutation: S181A, N182A, R185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: MATalpha2 / Plasmid: pAK2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6B184, UniProt: P0CY08*PLUS |
#5: 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: 49.5 % | ||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG400, 8 mM Co(NH3)6Cl3, 10 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: KODAK / Detector: CCD / Date: May 5, 1999 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 11201 / % possible obs: 92.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 44.9 Å2 / Rsym value: 0.03 / Net I/σ(I): 19.6 |
Reflection shell | Highest resolution: 2.3 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / Num. unique all: 11201 / Rsym value: 0.29 / % possible all: 53.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 48164 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 53.2 % / Rmerge(I) obs: 0.294 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.28 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1698228.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.1967 Å2 / ksol: 0.29234 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→24.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.255 / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.255 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.467 / Rfactor Rwork: 0.411 / Rfactor obs: 0.411 |