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Yorodumi- PDB-1ij2: GCN4-pVTL Coiled-coil Trimer with Threonine at the a(16) position -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ij2 | ||||||
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Title | GCN4-pVTL Coiled-coil Trimer with Threonine at the a(16) position | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | TRANSCRIPTION / GCN4 coiled coil | ||||||
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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Akey, D.L. / Malashkevich, V.N. / Kim, P.S. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Buried polar residues in coiled-coil interfaces. Authors: Akey, D.L. / Malashkevich, V.N. / Kim, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ij2.cif.gz | 31.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ij2.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 1ij2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ij2 ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ij2 | HTTPS FTP |
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-Related 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: 4018.702 Da / Num. of mol.: 3 / Fragment: COILED COIL REGION / Mutation: N16T / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT IS naturally found in SACCHAROMYCES CEREVISIAE (YEAST). The peptide is a variant of the yeast GCN4 coiled coil region made by solid phase synthesis. References: UniProt: P03069 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.76 Å3/Da / Density % sol: 30.3 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, 25 mM cadmium sulfate, 1 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Method: sparse matrix method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 9836 / Num. obs: 9570 / % possible obs: 97.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 5.8 / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 63455 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 664684.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.12 Å2 / ksol: 0.346 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.77 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 9
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.358 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.334 |