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Yorodumi- PDB-2wpz: GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wpz | ||||||
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Title | GCN4 leucine zipper mutant with two VxxNxxx motifs coordinating chloride | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | TRANSCRIPTION / AMINO-ACID BIOSYNTHESIS / TRANSCRIPTION REGULATION / ION COORDINATION / POLAR CORE RESIDUES / PROTEIN EXPORT / PHOSPHOPROTEIN / TAA / NUCLEUS / ACTIVATOR / COILED COIL / DNA-BINDING / TRIMERIC AUTOTRANSPORTER ADHESIN | ||||||
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: 1.25 Å | ||||||
Authors | Zeth, K. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Hernandez Alvarez, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: A Coiled-Coil Motif that Sequesters Ions to the Hydrophobic Core. Authors: Hartmann, M.D. / Ridderbusch, O. / Zeth, K. / Albrecht, R. / Testa, O. / Woolfson, D.N. / Sauer, G. / Dunin-Horkawicz, S. / Lupas, A.N. / Alvarez, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wpz.cif.gz | 56.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wpz.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpz ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpz | HTTPS FTP |
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-Related structure data
Related structure data | 2wpqC 2wprC 2wpsC 2wpyC 2wq0C 2wq1C 2wq2C 2wq3C 1gcmS S: Starting model for refinement C: citing same article (ref.) |
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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/peptide | Mass: 4018.619 Da / Num. of mol.: 3 / Fragment: COILED-COIL DOMAIN, RESIDUES 249-281 / Mutation: YES / Source method: obtained synthetically / Details: N-TERMINAL ACETYL GROUP / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 260 TO ASN ENGINEERED RESIDUE IN CHAIN A, ASN 264 TO VAL ...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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE |
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Crystal grow | Details: 30% PEG 4000, 200 MM NA-ACETATE, 0.1 M TRIS, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.009 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→40 Å / Num. obs: 20616 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.85 / % possible all: 87.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCM Resolution: 1.25→19.51 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.472 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→19.51 Å
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