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- PDB-3e1k: Crystal structure of Kluyveromyces lactis Gal80p in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3e1k
TitleCrystal structure of Kluyveromyces lactis Gal80p in complex with the acidic activation domain of Gal4p
Components
  • Galactose/lactose metabolism regulatory protein GAL80
  • Lactose regulatory protein LAC9
KeywordsTRANSCRIPTION / transctiption / repressor / trans-activation / Carbohydrate metabolism / DNA-binding / Galactose metabolism / Transcription regulation / Activator / Metal-binding / Nucleus / Zinc
Function / homology
Function and homology information


galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / DNA-templated transcription / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Gal80p, C-terminal domain / Gal4 dimerisation domain / Gal4-like dimerisation domain / : / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / : / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain ...Gal80p, C-terminal domain / Gal4 dimerisation domain / Gal4-like dimerisation domain / : / Fungal specific transcription factor domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / : / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Basic-leucine zipper domain superfamily / 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
Lactose regulatory protein LAC9 / Galactose/lactose metabolism regulatory protein GAL80
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsThoden, J.B. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Interaction between an Acidic Transcriptional Activator and Its Inhibitor: THE MOLECULAR BASIS OF Gal4p RECOGNITION BY Gal80p.
Authors: Thoden, J.B. / Ryan, L.A. / Reece, R.J. / Holden, H.M.
History
DepositionAug 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Lactose regulatory protein LAC9
C: Galactose/lactose metabolism regulatory protein GAL80
D: Lactose regulatory protein LAC9
E: Galactose/lactose metabolism regulatory protein GAL80
F: Lactose regulatory protein LAC9
G: Galactose/lactose metabolism regulatory protein GAL80
H: Lactose regulatory protein LAC9
I: Galactose/lactose metabolism regulatory protein GAL80
J: Lactose regulatory protein LAC9
K: Galactose/lactose metabolism regulatory protein GAL80
L: Lactose regulatory protein LAC9
M: Galactose/lactose metabolism regulatory protein GAL80
N: Lactose regulatory protein LAC9
O: Galactose/lactose metabolism regulatory protein GAL80
P: Lactose regulatory protein LAC9


Theoretical massNumber of molelcules
Total (without water)438,90216
Polymers438,90216
Non-polymers00
Water00
1
A: Galactose/lactose metabolism regulatory protein GAL80
B: Lactose regulatory protein LAC9
C: Galactose/lactose metabolism regulatory protein GAL80
D: Lactose regulatory protein LAC9


Theoretical massNumber of molelcules
Total (without water)109,7254
Polymers109,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-39 kcal/mol
Surface area31660 Å2
MethodPISA
2
E: Galactose/lactose metabolism regulatory protein GAL80
F: Lactose regulatory protein LAC9
G: Galactose/lactose metabolism regulatory protein GAL80
H: Lactose regulatory protein LAC9


Theoretical massNumber of molelcules
Total (without water)109,7254
Polymers109,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-42 kcal/mol
Surface area31750 Å2
MethodPISA
3
I: Galactose/lactose metabolism regulatory protein GAL80
J: Lactose regulatory protein LAC9
K: Galactose/lactose metabolism regulatory protein GAL80
L: Lactose regulatory protein LAC9


Theoretical massNumber of molelcules
Total (without water)109,7254
Polymers109,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-39 kcal/mol
Surface area31640 Å2
MethodPISA
4
M: Galactose/lactose metabolism regulatory protein GAL80
N: Lactose regulatory protein LAC9
O: Galactose/lactose metabolism regulatory protein GAL80
P: Lactose regulatory protein LAC9


Theoretical massNumber of molelcules
Total (without water)109,7254
Polymers109,7254
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-41 kcal/mol
Surface area31980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.100, 160.500, 132.600
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Galactose/lactose metabolism regulatory protein GAL80


Mass: 52174.902 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Gene: GAL80 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q06433
#2: Protein/peptide
Lactose regulatory protein LAC9


Mass: 2687.799 Da / Num. of mol.: 8 / Fragment: UNP residues 844-865 / Source method: obtained synthetically / Details: This sequence occurs naturally in yeast / References: UniProt: P08657

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES, 20-25% (w/v) pentaerythritol propoxylate 5/4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 6, 2006 / Details: mirrors
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 75005 / Num. obs: 75005 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2 / Num. unique all: 4730 / Rsym value: 0.249 / % possible all: 55.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
DMphasing
TNTrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NVW

2nvw


Resolution: 3→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 7561 -random
Rwork0.228 ---
all0.231 75005 --
obs0.231 74757 88.8 %-
Displacement parametersBiso max: 100 Å2 / Biso mean: 42.069 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26057 0 0 0 26057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.3
X-RAY DIFFRACTIONt_bond_d0.009

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