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Yorodumi- PDB-1mnn: Structure of the sporulation specific transcription factor Ndt80 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mnn | ||||||
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Title | Structure of the sporulation specific transcription factor Ndt80 bound to DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / IG FOLD / PROTEIN_DNA COMPLEX / TRANSCRIPTION-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 / MAD / Resolution: 1.4 Å | ||||||
Authors | Lamoureux, J.S. / Stuart, D. / Tsang, R. / Wu, C. / Glover, J.N. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Structure of the sporulation-specific transcription factor Ndt80 bound to DNA Authors: Lamoureux, J.S. / Stuart, D. / Tsang, R. / Wu, C. / Glover, J.N. | ||||||
History |
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Remark 999 | SEQUENCE These descrepancies exist and are allelic variation as this gene was cloned from a ...SEQUENCE These descrepancies exist and are allelic variation as this gene was cloned from a different strain of yeast than the deposited sequence |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mnn.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mnn.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1mnn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mnn_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 1mnn_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 1mnn_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1mnn_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/1mnn ftp://data.pdbj.org/pub/pdb/validation_reports/mn/1mnn | HTTPS FTP |
-Related 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: 4266.821 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4292.785 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 39163.121 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN (residues 1-340) 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: 2.32 Å3/Da / Density % sol: 47.08 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, calcium chloride, sodium chloride, bis-tris propane, DTT, spermine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98008 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 1, 2001 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98008 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. all: 88384 / Num. obs: 88384 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 38 % / Rsym value: 0.051 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.493 / % possible all: 97.8 |
Reflection | *PLUS Lowest resolution: 100 Å / Redundancy: 38 % / Num. measured all: 3338673 / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.493 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.4→81.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.283 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.06 / ESU R Free: 0.058 / 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: 19.621 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→81.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 1.42 Å |