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Yorodumi- PDB-3osf: The structure of protozoan parasite Trichomonas vaginalis Myb2 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3osf | ||||||
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Title | The structure of protozoan parasite Trichomonas vaginalis Myb2 in complex with MRE-2f-13 DNA | ||||||
Components |
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Keywords | transcription/DNA / transcription-DNA complex / Myb2 / R2R3 Domain / DNA binding protein / transcription factor / Nucleus | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / nucleus Similarity search - Function | ||||||
Biological species | Trichomonas vaginalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.032 Å | ||||||
Authors | Jiang, I. / Tsai, C.K. / Chen, S.C. / Wang, S.H. / Amiraslanov, I. / Chang, C.F. / Wu, W.J. / Tai, J.H. / Liaw, Y.C. / Huang, T.H. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2011 Title: Molecular basis of the recognition of the ap65-1 gene transcription promoter elements by a Myb protein from the protozoan parasite Trichomonas vaginalis. Authors: Jiang, I. / Tsai, C.K. / Chen, S.C. / Wang, S.H. / Amiraslanov, I. / Chang, C.F. / Wu, W.J. / Tai, J.H. / Liaw, Y.C. / Huang, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3osf.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3osf.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 3osf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/3osf ftp://data.pdbj.org/pub/pdb/validation_reports/os/3osf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14885.064 Da / Num. of mol.: 2 / Fragment: Myb2 R2R3 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_211210 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3) / References: UniProt: Q58HP3 #2: DNA chain | Mass: 3948.569 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 3993.639 Da / Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-IPA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M sodium cacodylate, 15% isopropanol, 25% PEG 4000, 10% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97622, 0.9788, 0.9790, 0.9686 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Jan 30, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal monochromato / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.03→50 Å / Num. all: 31872 / Num. obs: 31586 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.047 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.032→36.654 Å / SU ML: 0.29 / σ(F): 0.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.515 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.032→36.654 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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