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Yorodumi- PDB-2kdz: Structure of the R2R3 DNA binding domain of MYB1 protein from pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kdz | ||||||
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Title | Structure of the R2R3 DNA binding domain of MYB1 protein from protozoan parasite trichomonas vaginalis in complex with MRE-1/MRE-2R DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Myb1 / R2R3 Domain / DNA-binding / Nucleus / TRANSCRIPTION-DNA COMPLEX | ||||||
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 | SOLUTION NMR / simulated annealing, WATER REFINEMENT | ||||||
Authors | Lou, Y.C. / Wei, S.Y. / Rajasekaran, M. / Chou, C.C. / Hsu, H.M. / Tai, J.H. / Chen, C. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2009 Title: NMR structural analysis of DNA recognition by a novel Myb1 DNA-binding domain in the protozoan parasite Trichomonas vaginalis. Authors: Lou, Y.C. / Wei, S.Y. / Rajasekaran, M. / Chou, C.C. / Hsu, H.M. / Tai, J.H. / Chen, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kdz.cif.gz | 567.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kdz.ent.gz | 468.5 KB | Display | PDB format |
PDBx/mmJSON format | 2kdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kdz_validation.pdf.gz | 358.5 KB | Display | wwPDB validaton report |
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Full document | 2kdz_full_validation.pdf.gz | 487.4 KB | Display | |
Data in XML | 2kdz_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 2kdz_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/2kdz ftp://data.pdbj.org/pub/pdb/validation_reports/kd/2kdz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13218.242 Da / Num. of mol.: 1 / Fragment: Myb1 R2R3 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Strain: T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58HP2 |
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#2: DNA chain | Mass: 4929.254 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: DNA chain | Mass: 4862.188 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50 mM sodium chloride, 20 mM sodium phosphate, 5 mM sodium azide, 10 mM DTT, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.32 / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, WATER REFINEMENT / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1 |