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Yorodumi- PDB-2nrn: Self-assembly of coiled-coil tetramers in the 1.40 A structure of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nrn | ||||||
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Title | Self-assembly of coiled-coil tetramers in the 1.40 A structure of a leucine-zipper mutant | ||||||
Components | General control protein GCN4 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Coiled coils / tetramer / protein design / protein structure | ||||||
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: 1.4 Å | ||||||
Authors | Liu, J. / Lu, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Self-assembly of coiled-coil tetramers in the 1.40 A structure of a leucine-zipper mutant. Authors: Deng, Y. / Zheng, Q. / Liu, J. / Cheng, C.S. / Kallenbach, N.R. / Lu, M. | ||||||
History |
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Remark 999 | SEQUENCE These are designed sequence. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nrn.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nrn.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nrn ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nrn | HTTPS FTP |
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-Related structure data
Related structure data | 2ipzS S: Starting model for refinement |
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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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Details | The biological assembly is a tetramer. |
-Components
#1: Protein/peptide | Mass: 3902.606 Da / Num. of mol.: 4 / Fragment: GCN4 leucine zipper / Mutation: E254A, E268A, K275A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03069 #2: Chemical | ChemComp-PO4 / #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: 1.95 Å3/Da / Density % sol: 37 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M sodium citrate, 1M ammonium dihydrophosphate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→43.94 Å / Num. all: 22711 / Num. obs: 22711 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.4→1.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3 / Num. unique all: 1435 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IPZ Resolution: 1.4→43.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.018 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.07 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→43.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.433 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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