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- PDB-3v5r: Crystal structure of the unliganded form of Gal3p -

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Basic information

Entry
Database: PDB / ID: 3v5r
TitleCrystal structure of the unliganded form of Gal3p
ComponentsProtein GAL3
KeywordsTRANSCRIPTION / GHMP superfamily / Transcription transducer / Gal80p
Function / homology
Function and homology information


galactokinase activity / maintenance of protein location / galactose metabolic process / positive regulation of transcription from RNA polymerase II promoter by galactose / transcription regulator complex / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...de novo design (two linked rop proteins) - #340 / Alpha-Beta Plaits - #3170 / Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / de novo design (two linked rop proteins) / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsLavy, T. / Kumar, P.R. / He, H. / Joshua-Tor, L.
CitationJournal: Genes Dev. / Year: 2012
Title: The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation.
Authors: Lavy, T. / Kumar, P.R. / He, H. / Joshua-Tor, L.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein GAL3
B: Protein GAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,62429
Polymers113,0302
Non-polymers2,59427
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-363 kcal/mol
Surface area40280 Å2
MethodPISA
2
A: Protein GAL3
B: Protein GAL3
hetero molecules

A: Protein GAL3
B: Protein GAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,24758
Polymers226,0604
Non-polymers5,18754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
Buried area20060 Å2
ΔGint-781 kcal/mol
Surface area77800 Å2
MethodPISA
3
A: Protein GAL3
B: Protein GAL3
hetero molecules

A: Protein GAL3
B: Protein GAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,24758
Polymers226,0604
Non-polymers5,18754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area20690 Å2
ΔGint-781 kcal/mol
Surface area77170 Å2
MethodPISA
4
A: Protein GAL3
hetero molecules

A: Protein GAL3
hetero molecules

B: Protein GAL3
hetero molecules

B: Protein GAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,24758
Polymers226,0604
Non-polymers5,18754
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area12560 Å2
ΔGint-668 kcal/mol
Surface area85300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.359, 153.359, 118.591
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-527-

SO4

21A-624-

HOH

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Components

#1: Protein Protein GAL3


Mass: 56514.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GAL3, YDR009W, YD8119.14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIPL / References: UniProt: P13045
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 10 mM MgCl2, 50 mM MES, 1.85M Li2SO4, pH 5.9, 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
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.099→132.453 Å / Num. all: 94018 / Num. obs: 93763 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.0988-2.1277197
2.1227-2.14771100
2.1477-2.17391100
2.1739-2.20141100
2.2014-2.23031100
2.2303-2.26091100
2.2609-2.29321100
2.2932-2.32741100
2.3274-2.36381100
2.3638-2.40251100
2.4025-2.4441100
2.444-2.48841100
2.4884-2.53631100
2.5363-2.5881100
2.588-2.64431100
2.6443-2.70581100
2.7058-2.77351100
2.7735-2.84841100
2.8484-2.93221100
2.9322-3.02691100
3.0269-3.1351100
3.135-3.26051100
3.2605-3.40891100
3.4089-3.58851100
3.5885-3.81331100
3.8133-4.10751100
4.1075-4.52061100
4.5206-5.1741100
5.174-6.51591100
6.5159-46.9186199

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S. cerevisiae Gal1p (pdb code: 2AJ4)

2aj4


Resolution: 2.099→46.907 Å / SU ML: 0.52 / σ(F): 1.34 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 4708 5.02 %Throughout
Rwork0.1697 ---
obs0.1713 93747 99.71 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.002 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.8009 Å20 Å2-0 Å2
2--17.8009 Å20 Å2
3---3.5636 Å2
Refinement stepCycle: LAST / Resolution: 2.099→46.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7827 0 135 778 8740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078257
X-RAY DIFFRACTIONf_angle_d111210
X-RAY DIFFRACTIONf_dihedral_angle_d13.2422996
X-RAY DIFFRACTIONf_chiral_restr0.0751225
X-RAY DIFFRACTIONf_plane_restr0.0041447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0988-2.12270.27911750.21622860X-RAY DIFFRACTION97
2.1227-2.14770.22151540.21012919X-RAY DIFFRACTION100
2.1477-2.17390.22681640.19382932X-RAY DIFFRACTION100
2.1739-2.20140.23231550.19632966X-RAY DIFFRACTION100
2.2014-2.23030.23331550.19722930X-RAY DIFFRACTION100
2.2303-2.26090.25471430.19332942X-RAY DIFFRACTION100
2.2609-2.29320.25351740.19842920X-RAY DIFFRACTION100
2.2932-2.32740.26951510.1962967X-RAY DIFFRACTION100
2.3274-2.36380.24641580.19762962X-RAY DIFFRACTION100
2.3638-2.40250.22911410.19842936X-RAY DIFFRACTION100
2.4025-2.4440.23011410.18512957X-RAY DIFFRACTION100
2.444-2.48840.25471660.18422960X-RAY DIFFRACTION100
2.4884-2.53630.22381450.19082911X-RAY DIFFRACTION100
2.5363-2.5880.23891560.19152974X-RAY DIFFRACTION100
2.588-2.64430.24491440.19042999X-RAY DIFFRACTION100
2.6443-2.70580.24961530.19742950X-RAY DIFFRACTION100
2.7058-2.77350.28611660.20462958X-RAY DIFFRACTION100
2.7735-2.84840.24651420.1992994X-RAY DIFFRACTION100
2.8484-2.93220.24161570.20352952X-RAY DIFFRACTION100
2.9322-3.02690.24521490.1992970X-RAY DIFFRACTION100
3.0269-3.1350.22231570.19822982X-RAY DIFFRACTION100
3.135-3.26050.20711560.19032956X-RAY DIFFRACTION100
3.2605-3.40890.22061690.18212996X-RAY DIFFRACTION100
3.4089-3.58850.19241560.16442995X-RAY DIFFRACTION100
3.5885-3.81330.16541690.14032946X-RAY DIFFRACTION100
3.8133-4.10750.17461750.13232972X-RAY DIFFRACTION100
4.1075-4.52060.13681480.12193029X-RAY DIFFRACTION100
4.5206-5.1740.13721290.12643040X-RAY DIFFRACTION100
5.174-6.51590.18951810.16553031X-RAY DIFFRACTION100
6.5159-46.91860.17941790.16943133X-RAY DIFFRACTION99
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)
11.9073-0.43930.59170.5269-0.37790.8498-0.0333-0.12740.16710.01620.02530.0511-0.1174-0.18150.06430.0659-0.0495-0.01450.1261-0.01460.073790.78664.724539.3388
21.20710.3552-0.12930.646-0.1620.6467-0.0284-0.1249-0.03770.0424-0.05130.0160.03830.0395-0.02490.034-0.06210.01150.06560.03920.0399106.767248.015155.9074
30.6096-0.02640.12110.43640.10551.62530.0777-0.0497-0.14120.1804-0.10790.13460.452-0.19630.08330.2922-0.20010.05160.3914-0.09420.1597101.845260.934692.9944
41.4601-0.0517-0.55910.787-0.23221.40140.036-0.16910.10860.1842-0.09660.1774-0.1025-0.1903-0.11640.1276-0.08290.03860.3654-0.09360.132795.815681.881574.3646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resseq 19:240) or (chain 'A'
2X-RAY DIFFRACTION2(chain 'A' and resseq 241:510)
3X-RAY DIFFRACTION3(chain 'B' and resseq 19:240) or (chain 'B'
4X-RAY DIFFRACTION4(chain 'B' and resseq 241:510)

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