+Open data
-Basic information
Entry | Database: PDB / ID: 6o19 | ||||||
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Title | Crystal Structure of Pho7 complex with pho1 promoter site 2 | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Zn2Cys6 / Zinc binuclear cluster transcription factor / transcription factor-DNA complex / Pho7 / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin ...intracellular phosphate ion homeostasis / cellular response to phosphate starvation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to starvation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.596 Å | ||||||
Authors | Garg, A. / Goldgur, Y. / Shuman, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol.Cell.Biol. / Year: 2019 Title: Structure of Fission Yeast Transcription Factor Pho7 Bound topho1Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis. Authors: Garg, A. / Goldgur, Y. / Sanchez, A.M. / Schwer, B. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o19.cif.gz | 60.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o19.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/6o19 ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o19 | HTTPS FTP |
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-Related structure data
Related structure data | 6e33S 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: Protein | Mass: 6763.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: pi067, SPBC27B12.11c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13658 | ||
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#2: DNA chain | Mass: 6149.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) | ||
#3: DNA chain | Mass: 6112.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) | ||
#4: Chemical | #5: 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: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris.HCl pH 8.0, 0.2M NaOAc, 35% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.596→50 Å / Num. obs: 28959 / % possible obs: 97.9 % / Redundancy: 4 % / CC1/2: 1 / Rpim(I) all: 0.027 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.596→1.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.979 / Num. unique obs: 1429 / Rpim(I) all: 0.131 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+33 / Resolution: 1.596→43.571 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.596→43.571 Å
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Refine LS restraints |
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LS refinement shell |
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