+Open data
-Basic information
Entry | Database: PDB / ID: 2evj | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of an Ndt80-DNA complex (MSE mutant mA9C) | ||||||
Components |
| ||||||
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: 1.89 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2evj.cif.gz | 101.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2evj.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 2evj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2evj_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2evj_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 2evj_validation.xml.gz | 17 KB | Display | |
Data in CIF | 2evj_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/2evj ftp://data.pdbj.org/pub/pdb/validation_reports/ev/2evj | HTTPS FTP |
-Related structure data
Related structure data | 2etwC 2euvC 2euwC 2euxC 2euzC 2evfC 2evgC 2evhC 2eviC 1mnnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: DNA chain | Mass: 4242.796 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 1 |
---|---|
#2: DNA chain | Mass: 4317.798 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MUTANT MSE DNA STRAND 2 |
#3: Protein | Mass: 39590.527 Da / Num. of mol.: 1 / Fragment: NDT80 DNA BINDING DOMAIN / Mutation: s146g, i200t 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.35 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
|
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0093 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 8, 2001 |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal sagittal focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→81.65 Å / Num. all: 35986 / Num. obs: 35750 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.89→1.97 Å / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB 1MNN - MINUS DNA AT SEQUENCE CHANGES AND 1 BASEPAIR ADJACENT TO THOSE CHANGES Resolution: 1.89→35.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.714 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 18.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→35.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.89→1.941 Å / Total num. of bins used: 20
|