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

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Basic information

Entry
Database: PDB / ID: 3btu
TitleCrystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K]
ComponentsGalactose/lactose metabolism regulatory protein GAL80
KeywordsTRANSCRIPTION / Eukaryotic transcription complex / Acetylation / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Repressor / 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 / MIRAS / Resolution: 2.85 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 30, 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
C: Galactose/lactose metabolism regulatory protein GAL80
D: Galactose/lactose metabolism regulatory protein GAL80
E: Galactose/lactose metabolism regulatory protein GAL80
F: Galactose/lactose metabolism regulatory protein GAL80


Theoretical massNumber of molelcules
Total (without water)291,9266
Polymers291,9266
Non-polymers00
Water00
1
A: Galactose/lactose metabolism regulatory protein GAL80
B: Galactose/lactose metabolism regulatory protein GAL80


Theoretical massNumber of molelcules
Total (without water)97,3092
Polymers97,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-19.3 kcal/mol
Surface area31510 Å2
MethodPISA
2
C: Galactose/lactose metabolism regulatory protein GAL80
D: Galactose/lactose metabolism regulatory protein GAL80


Theoretical massNumber of molelcules
Total (without water)97,3092
Polymers97,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-20 kcal/mol
Surface area31420 Å2
MethodPISA
3
E: Galactose/lactose metabolism regulatory protein GAL80
F: Galactose/lactose metabolism regulatory protein GAL80


Theoretical massNumber of molelcules
Total (without water)97,3092
Polymers97,3092
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-17.9 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)495.320, 84.862, 66.460
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Galactose/lactose metabolism regulatory protein GAL80


Mass: 48654.355 Da / Num. of mol.: 6 / Mutation: E351K
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.1M CAPS, 0.2M NaCl, 20% PEG 8000, 50mM DTT, 4% Gamma-butyrolactone, 0.2M Sodium formate, 9% Sucrose, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONAPS 19-ID21.2519
SYNCHROTRONNSLS X2530.9792
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
ADSC QUANTUM 3153CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.25191
30.97921
ReflectionResolution: 2.85→50 Å / Num. all: 57929 / Num. obs: 54557 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 70.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.2
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.372 / % possible all: 83

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.838 / SU B: 48.543 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.6 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 5497 10.1 %RANDOM
Rwork0.228 ---
obs-49054 85.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.676 Å2
Baniso -1Baniso -2Baniso -3
1--6.09 Å20 Å20.37 Å2
2---0.5 Å20 Å2
3---6.7 Å2
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18389 0 0 0 18389
LS refinement shellResolution: 2.85→2.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 104 -
Rwork0.332 1023 -
obs--23.88 %
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)
12.54461.32890.64461.12380.2787-0.32530.1173-0.3420.0366-0.0962-0.1336-0.26820.14450.2450.00010.7492-0.00830.08480.8065-0.04541.0866110.05738.37833.4308
21.2119-0.3893-0.61241.3188-0.67750.8447-0.0692-0.3342-0.0221-0.08670.0169-0.2743-0.04350.0607-00.57050.04720.00750.4523-0.10870.65385.265533.578644.2849
30.71150.26610.81560.5296-0.03931.63110.16710.21650.1852-0.0405-0.1026-0.1567-0.16560.095900.6553-0.01280.05510.5367-0.14750.871690.394638.690731.2586
40.92440.07231.17170.2609-0.77240.3030.09010.11440.0539-0.03590.3298-0.2712-0.0506-0.57660.00010.7620.16910.10261.02890.07520.942939.554737.92160.3719
51.5430.3769-0.22260.9544-0.20511.4380.04850.15730.00390.01410.1540.09720.0608-0.14830.00010.56830.02630.04010.4033-0.13850.632863.605834.43347.897
60.4817-0.73380.3990.6788-0.86262.5749-0.0263-0.2463-0.1978-0.07110.2055-0.3251-0.0368-0.413200.58860.05070.05840.5004-0.12460.775759.030334.989462.2647
70.26860.8816-1.94980.37430.40121.3903-0.0556-0.1959-0.31040.2153-0.1715-0.2949-0.00621.0179-00.69580.1378-0.31191.13440.22191.0047107.041673.148762.6906
80.71850.23080.32171.9522-0.11120.7975-0.08760.06480.1170.1638-0.0689-0.20170.02180.2512-00.63270.0929-0.02140.4586-0.05570.532586.94479.35445.298
90.88780.6395-1.30180.49540.38852.03060.1189-0.39720.050.1723-0.0298-0.33640.12040.40660.00020.81780.1532-0.06490.6522-0.05860.639887.529374.481959.3982
101.5642-0.292-0.24770.22150.27870.3523-0.1791-0.01890.1288-0.02890.3191-0.26970.0726-0.6125-00.7172-0.199-0.17970.89770.14750.692946.695678.206617.5961
111.1999-0.34910.05551.154-0.29411.6629-0.1875-0.23620.0387-0.03960.17420.10940.0129-0.1736-00.61570.0502-0.00010.4325-0.07170.502267.057680.321235.8938
120.5222-0.29650.21740.09330.05312.1322-0.00850.18090.0314-0.3020.21770.31120.1673-0.2391-0.00010.6222-0.0361-0.06060.47-0.00510.540566.069679.310720.9334
130.9131-0.55460.42631.0219-1.26960.21290.38780.5244-0.0425-0.02520.19230.07270.503-0.57650.00040.9642-0.4232-0.4081.46450.22670.862926.0175-16.9779-15.6419
14-0.3259-0.3634-0.5270.1406-0.54040.54670.24010.2995-0.2607-0.00470.22420.10420.0225-0.90630.00270.557-0.209-0.07921.9750.61590.660119.69915.6967-1.0269
15-0.0641-0.1171.04590.5191.03760.43690.497-0.18740.2514-0.17330.1736-0.0740.3937-0.61790.00020.8856-0.3509-0.23771.74070.52680.795924.36652.5643-14.5446
160.26560.5866-0.14980.5458-0.8162-0.50460.17120.02770.29810.21040.6330.7899-0.2872-0.76660.00041.07050.48350.50171.35990.34271.39221.353949.104221.5619
170.7549-0.13640.1883-0.3564-0.2375-0.2365-0.04110.24270.3252-0.06450.51920.10180.2592-1.05670.00010.60430.20380.08022.06570.64390.604118.879226.43045.8875
180.56440.0274-0.77480.9598-0.1399-0.19020.33230.15560.3890.22560.1990.20950.0255-0.4616-00.71590.30870.20061.67240.45560.741219.873629.467320.1548
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
7X-RAY DIFFRACTION7chain C and resid 1:155C1 - 155
8X-RAY DIFFRACTION8chain C and resid 156:330C156 - 330
9X-RAY DIFFRACTION9chain C and resid 345:435C345 - 435
10X-RAY DIFFRACTION10chain D and resid 1:155D1 - 155
11X-RAY DIFFRACTION11chain D and resid 156:330D156 - 330
12X-RAY DIFFRACTION12chain D and resid 345:435D345 - 435
13X-RAY DIFFRACTION13chain E and resid 1:155E1 - 155
14X-RAY DIFFRACTION14chain E and resid 156:330E156 - 330
15X-RAY DIFFRACTION15chain E and resid 345:435E345 - 435
16X-RAY DIFFRACTION16chain F and resid 1:155F1 - 155
17X-RAY DIFFRACTION17chain F and resid 156:330F156 - 330
18X-RAY DIFFRACTION18chain F and resid 345:435F345 - 435

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