+Open data
-Basic information
Entry | Database: PDB / ID: 2ccf | ||||||
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Title | Antiparallel Configuration of pLI E20S | ||||||
Components | General control protein GCN4 | ||||||
Keywords | FOUR HELIX BUNDLE / ANTIPARALLEL / PARALLEL / PLI / DNA-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION / TRANSCRIPTION REGULATION / ACTIVATOR / AMINO-ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Yadav, M.K. / Leman, L.J. / Price, D.J. / Brooks 3rd, C.L. / Stout, C.D. / Ghadiri, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent- ...Title: Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Authors: Yadav, M.K. / Leman, L.J. / Price, D.J. / Brooks 3rd, C.L. / Stout, C.D. / Ghadiri, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ccf.cif.gz | 24.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ccf.ent.gz | 18.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ccf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2ccf ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2ccf | HTTPS FTP |
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-Related structure data
Related structure data | 1w5hC 1w5jC 1w5kC 1w5lC 2cceC 2ccnC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 4030.802 Da / Num. of mol.: 2 / Fragment: RESIDUES 249-281 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.09 Å3/Da / Density % sol: 35 % |
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Crystal grow | pH: 10 / Details: 100MM CAPS PH 10.5, 30% PEG 400 |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 7769 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.06 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→52.13 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.858 / SU B: 2.563 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R-FREE IS HIGHER THEN EXPECTED BUT CONSISTENT WITH RELATED SEQUENCES IN SAME LATTICE. ELECTRON DENSITY MAPS ARE EXCELLENT.
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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: 28.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→52.13 Å
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Refine LS restraints |
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