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- PDB-3btv: Crystal structure of the super-repressor mutant of Gal80p from Sa... -

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Basic information

Entry
Database: PDB / ID: 3btv
TitleCrystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R]
ComponentsGalactose/lactose metabolism regulatory protein GAL80
KeywordsTRANSCRIPTION / eukaryotic transcription repressor / Acetylation / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Transcription regulation
Function / homology
Function and homology information


regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / DNA binding ...regulation of transcription from RNA polymerase II promoter by galactose / kinase inhibitor activity / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription repressor complex / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Gal80p, C-terminal domain / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / Gal80p, C-terminal domain / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Galactose/lactose metabolism regulatory protein GAL80
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKumar, P.R. / Joshua-Tor, L.
CitationJournal: Science / Year: 2008
Title: NADP regulates the yeast GAL induction system.
Authors: Kumar, P.R. / Yu, Y. / Sternglanz, R. / Johnston, S.A. / Joshua-Tor, L.
History
DepositionDec 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galactose/lactose metabolism regulatory protein GAL80
B: Galactose/lactose metabolism regulatory protein GAL80


Theoretical massNumber of molelcules
Total (without water)97,5092
Polymers97,5092
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-13.5 kcal/mol
Surface area34100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.087, 103.947, 106.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Galactose/lactose metabolism regulatory protein GAL80


Mass: 48754.434 Da / Num. of mol.: 2 / Mutation: G301R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GAL80 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P04387
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BTU

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
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2867 5.04 %RANDOM
Rwork0.215 ---
obs-56866 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.1→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 0 167 6380
LS refinement shellResolution: 2.1→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 137 -
Rwork0.2735 2636 -
obs--99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.069-0.65050.25881.8160.08780.65750.09270.0428-0.289-0.5493-0.11510.2792-0.00310.1049-0.00190.4281-0.0241-0.04050.21010.00330.216217.30679.471230.4042
20.71750.75750.57011.2531-0.46570.3489-0.115-0.2615-0.166-0.06470.0768-0.2070.05090.0346-0.00080.24860.02370.06570.24360.07870.353826.888212.096756.7118
31.355-0.78290.21780.8827-0.2061.41620.065-0.0384-0.3633-0.37130.00710.21960.1006-0.31450.00040.2778-0.02830.01470.22580.10470.424815.02493.7649.3364
40.96450.49580.41931.107-0.84050.8386-0.1268-0.99080.00180.6656-0.10630.0684-0.4351-0.8617-0.55690.78450.2040.03631.1097-0.17030.16331.307523.1959104.5295
50.80190.43641.35740.46460.27571.63910.0396-0.5242-0.03430.1809-0.02-0.10580.0735-0.341900.34030.0480.06630.43990.07610.326628.810913.647878.2788
60.89290.5780.34550.5398-0.21291.8182-0.1243-0.57630.08450.1925-0.12570.0911-0.303-0.1905-0.00010.3990.1523-0.00840.4763-0.11840.212336.359925.951885.2736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 1:155A1 - 155
2X-RAY DIFFRACTION2chain A and resid 156:330A156 - 330
3X-RAY DIFFRACTION3chain A and resid 345:435A345 - 435
4X-RAY DIFFRACTION4chain B and resid 1:155B1 - 155
5X-RAY DIFFRACTION5chain B and resid 156:330B156 - 330
6X-RAY DIFFRACTION6chain B and resid 345:435B345 - 435

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