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Yorodumi- PDB-1yo5: Analysis of the 2.0A crystal structure of the protein-DNA complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yo5 | ||||||
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Title | Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / ETS / PROTEIN-DNA Complex / DOUBLE HELIX / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of cell fate commitment / negative regulation of cell fate commitment / lung goblet cell differentiation / epithelial cell fate commitment / glandular epithelial cell development / intestinal epithelial cell development / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific ...positive regulation of cell fate commitment / negative regulation of cell fate commitment / lung goblet cell differentiation / epithelial cell fate commitment / glandular epithelial cell development / intestinal epithelial cell development / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, Y. / Feng, L. / Said, M. / Balderman, S. / Fayazi, Z. / Liu, Y. / Ghosh, D. / Gulick, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Analysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site Authors: Wang, Y. / Feng, L. / Said, M. / Balderman, S. / Fayazi, Z. / Liu, Y. / Ghosh, D. / Gulick, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yo5.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yo5.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yo5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yo5_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 1yo5_full_validation.pdf.gz | 439.3 KB | Display | |
Data in XML | 1yo5_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 1yo5_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yo5 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yo5 | HTTPS FTP |
-Related structure data
Related structure data | 1duxS S: Starting model for refinement |
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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
#1: DNA chain | Mass: 4046.645 Da / Num. of mol.: 1 / Fragment: Sense Strand of E site / Source method: obtained synthetically Details: This sequence occurs naturally in humans. DNA substrate for protein is synthesized chemically and purified through chromatography |
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#2: DNA chain | Mass: 3895.563 Da / Num. of mol.: 1 / Fragment: Antisense Strand of E site / Source method: obtained synthetically Details: This sequence occurs naturally in humans. DNA substrate for protein is synthesized chemically and purified through chromatography |
#3: Protein | Mass: 11587.606 Da / Num. of mol.: 1 / Fragment: PDEF C-terminal Ets domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDEF / Plasmid: PET-GST-T-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Lambda DE3) / References: UniProt: O95238 |
#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: 2.3 Å3/Da / Density % sol: 46.6 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 4000, Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 9, 2004 / Details: Osmic Max-FLUX confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.9 Å / Num. all: 11755 / Num. obs: 11176 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Biso Wilson estimate: 25.73 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.6 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DUX Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.742 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.592 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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