+Open data
-Basic information
Entry | Database: PDB / ID: 2bni | ||||||
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Title | pLI mutant E20C L16G Y17H, antiparallel | ||||||
Components | GENERAL CONTROL PROTEIN GCN4 | ||||||
Keywords | FOUR HELIX BUNDLE / ANTIPARALLEL FOUR HELIX BUNDLE ACYL TRANSFERASE | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / 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 / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / : / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / 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: 1.5 Å | ||||||
Authors | Yadav, M.K. / Leman, L.J. / Stout, C.D. / Ghadiri, M.R. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides Authors: Yadav, M.K. / Redman, J.E. / Leman, L.J. / Alvarez-Gutierrez, J.M. / Zhang, Y. / 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 | 2bni.cif.gz | 35.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bni.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bni_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 2bni_full_validation.pdf.gz | 441.7 KB | Display | |
Data in XML | 2bni_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 2bni_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bni ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bni | HTTPS FTP |
-Related structure data
Related structure data | 1untC 1unuC 1unvC 1unwC 1unxC 1unyC 1unzC 1uo0C 1uo1C 1uo2C 1uo3C 1uo4C 1uo5C 1w5gC 1w5iC 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: 4100.854 Da / Num. of mol.: 4 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P03069 #2: 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: 1.8 Å3/Da / Density % sol: 30.6 % |
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Crystal grow | Method: vapor diffusion, sitting drop Details: SITTING DROP WITH 200NL 20% PEG 3350 0.2M POTASSIUM THIOCYANATE AND 200NL 20MG/ML PEPTIDE STOCK IN WATER. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97 |
Detector | Date: Dec 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 89229 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 5.17 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→149.07 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MAPS WERE VERY SHARP AND ABA GROUPS WERE CLEAR. R FACTOR A LITTLE HIGHER THAN EXPECTED, ALTHOUGH CONSISTENT WITH OTHER STRUCTURES. SPOTS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MAPS WERE VERY SHARP AND ABA GROUPS WERE CLEAR. R FACTOR A LITTLE HIGHER THAN EXPECTED, ALTHOUGH CONSISTENT WITH OTHER STRUCTURES. SPOTS WERE A LITTLE STREAKY WITH AN ICE RING, BUT DATA ENDED UP PROCESSING WELL.THIS PEPTIDE IS AN ACTIVE AMINOACYL TRANSFERASE AND WILL HOPEFULLY BE FOUND TO HAVE SOME SORT OF BINDING AND CATALYTIC ABILITY.
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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: 17.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→149.07 Å
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