+Open data
-Basic information
Entry | Database: PDB / ID: 1a0a | ||||||
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Title | PHOSPHATE SYSTEM POSITIVE REGULATORY PROTEIN PHO4/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / BASIC HELIX LOOP HELIX / COMPLEX (TRANSCRIPTION FACTOR-DNA) / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of phosphate metabolic process / cellular response to phosphate starvation / sequence-specific DNA binding / protein dimerization activity / chromatin remodeling / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Shimizu, T. / Toumoto, A. / Ihara, K. / Shimizu, M. / Kyogoku, Y. / Ogawa, N. / Oshima, Y. / Hakoshima, T. | ||||||
Citation | Journal: EMBO J. / Year: 1997 Title: Crystal structure of PHO4 bHLH domain-DNA complex: flanking base recognition. Authors: Shimizu, T. / Toumoto, A. / Ihara, K. / Shimizu, M. / Kyogoku, Y. / Ogawa, N. / Oshima, Y. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a0a.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a0a.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/1a0a ftp://data.pdbj.org/pub/pdb/validation_reports/a0/1a0a | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5212.386 Da / Num. of mol.: 1 / Fragment: UPSTREAM ACTIVATION SITE P2 / Source method: obtained synthetically / Keywords: FRAGMENT UPSTREAM ACTIVATION SITE P2 | ||
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#2: DNA chain | Mass: 5203.373 Da / Num. of mol.: 1 / Fragment: UPSTREAM ACTIVATION SITE P2 / Source method: obtained synthetically / Keywords: FRAGMENT: UPSTREAM ACTIVATION SITE P2 | ||
#3: Protein | Mass: 7104.062 Da / Num. of mol.: 2 / Fragment: DNA BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: FRAGMENT: DNA BINDING DOMAIN / References: UniProt: P07270 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 71 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 3.6 Details: VAPOR DIFFUSION METHOD: DROP-0.4MM PROTEIN, 0.2MM DNA, 1% PEG6K, 20MM NACITRATE (PH3.6), RESERVOIR-1% PEG6K, 20MM NACITRATE(PH3.6), vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 71 % | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 9398 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.5 / % possible all: 80.4 |
Reflection | *PLUS Highest resolution: 2.8 Å / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Num. measured all: 36943 / Biso Wilson estimate: 26.2 Å2 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 76.8 % / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters | Biso mean: 28.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 12.5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / % reflection Rfree: 13.1 % |