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- PDB-3btv: Crystal structure of the super-repressor mutant of Gal80p from Sa... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3btv | ||||||
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Title | Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R] | ||||||
![]() | Galactose/lactose metabolism regulatory protein GAL80 | ||||||
![]() | TRANSCRIPTION / eukaryotic transcription repressor / Acetylation / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Transcription regulation | ||||||
Function / homology | ![]() regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / negative regulation of phosphorylation / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / nucleotide binding / negative regulation of transcription by RNA polymerase II ...regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / negative regulation of phosphorylation / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / nucleotide binding / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, P.R. / Joshua-Tor, L. | ||||||
![]() | ![]() Title: NADP regulates the yeast GAL induction system. Authors: Kumar, P.R. / Yu, Y. / Sternglanz, R. / Johnston, S.A. / Joshua-Tor, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.2 KB | Display | ![]() |
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PDB format | ![]() | 135.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.8 KB | Display | ![]() |
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Full document | ![]() | 463.7 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 44 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3btsC ![]() 3btuSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48754.434 Da / Num. of mol.: 2 / Mutation: G301R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: GAL80 / Plasmid: PET28a / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 3350, 0.15M Sodium Fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 57002 / Num. obs: 56922 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 42.556 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.06 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3BTU Resolution: 2.1→46.61 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.355 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.201 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.61 Å
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LS refinement shell | Resolution: 2.1→2.14 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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