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Open data
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Basic information
Entry | Database: PDB / ID: 3crp | ||||||
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Title | A heterospecific leucine zipper tetramer | ||||||
![]() | (GCN4 leucine zipper) x 2 | ||||||
![]() | PROTEIN BINDING / Coiled coils / anti-parallel tetramer / protein complex / heterospecific interaction / Activator / Amino-acid biosynthesis / DNA-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation | ||||||
Function / homology | ![]() 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 / transcription regulator complex / sequence-specific DNA binding / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. | ||||||
![]() | ![]() Title: A heterospecific leucine zipper tetramer. Authors: Deng, Y. / Liu, J. / Zheng, Q. / Li, Q. / Kallenbach, N.R. / Lu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.7 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.6 KB | Display | ![]() |
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Full document | ![]() | 431.8 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ck4C ![]() 2nrnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assemblies are a hetero-tetramer, and a homo-tetramer generated by symmtry element. |
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Components
#1: Protein/peptide | Mass: 3902.606 Da / Num. of mol.: 2 / Fragment: UNP residues 251-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Production host: ![]() ![]() #2: Protein/peptide | Mass: 3902.540 Da / Num. of mol.: 3 / Fragment: UNP residues 251-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GCN4, AAS3, ARG9 / Plasmid: pAE4 / Production host: ![]() ![]() #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.8 Details: 0.1M Tris-HCl, 0.05M magnesium chloride, 13% PEG 4000, pH 9.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 18, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25.1 Å / Num. all: 19756 / Num. obs: 19756 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 9 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1281 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NRN Resolution: 1.7→25.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.122 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: Isotropic with TLS group assigned for each peptide chain Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.109 / 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: 37.345 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.702→1.746 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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