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Yorodumi- PDB-2euv: Principles of protein-DNA recognition revealed in the structural ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2euv | ||||||
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Title | Principles of protein-DNA recognition revealed in the structural analysis of Ndt80-MSE DNA complexes | ||||||
Components |
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Keywords | CELL CYCLE/DNA / BETA-BARREL / IG-FOLD TRANSCRIPTION FACTOR / CELL CYCLE-DNA COMPLEX | ||||||
Function / homology | Function and homology information nuclear chromosome / meiotic cell cycle / sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / positive regulation of transcription by RNA polymerase II Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å | ||||||
Authors | Lamoureux, J.S. / Glover, J.N. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Principles of Protein-DNA Recognition Revealed in the Structural Analysis of Ndt80-MSE DNA Complexes. Authors: Lamoureux, J.S. / Glover, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2euv.cif.gz | 97.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2euv.ent.gz | 69.2 KB | Display | PDB format |
PDBx/mmJSON format | 2euv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/2euv ftp://data.pdbj.org/pub/pdb/validation_reports/eu/2euv | HTTPS FTP |
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-Related structure data
Related structure data | 2etwC 2euwC 2euxC 2euzC 2evfC 2evgC 2evhC 2eviC 2evjC 1mnnS 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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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 4241.808 Da / Num. of mol.: 1 / Mutation: I200T / Source method: obtained synthetically / Details: vG1C MSE DNA strand 1 |
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#2: DNA chain | Mass: 4316.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: vG1C MSE DNA strand 2 |
#3: Protein | Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: Ndt80 DNA-binding Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ndt80 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38830 |
#4: 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: 2.27 Å3/Da / Density % sol: 45.92 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 400, 50 mM bis-tris-propane pH 7.0, 100 mM NaCl, 50 mM CaCl2, and 2 mM DTT. 1:1 Molar ratio protein:DNA, protein at 20mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.072158 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2003 / Details: MIRRORS |
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072158 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.47 Å / Num. all: 35256 / Num. obs: 35256 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.2 / Num. unique all: 5080 / Rsym value: 0.526 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES Resolution: 1.94→16.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.224 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.146 / 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: 26.702 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→16.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 Å / Total num. of bins used: 20
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