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- PDB-5oa6: Crystal structure of ScGas2 in complex with compound 12 -

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Basic information

Entry
Database: PDB / ID: 5oa6
TitleCrystal structure of ScGas2 in complex with compound 12
Components1,3-beta-glucanosyltransferase GAS2
KeywordsTRANSFERASE
Function / homology
Function and homology information


1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / fungal-type cell wall beta-glucan biosynthetic process / ascospore wall assembly / fungal-type cell wall organization / fungal-type cell wall / fungal-type vacuole / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / plasma membrane / cytoplasm
Similarity search - Function
Glucanosyltransferase / Glucanosyltransferase / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-9PT / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDelso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / Van Aalten, D. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R.
CitationJournal: ChemMedChem / Year: 2018
Title: Inhibitors against Fungal Cell Wall Remodeling Enzymes.
Authors: Delso, I. / Valero-Gonzalez, J. / Gomollon-Bel, F. / Castro-Lopez, J. / Fang, W. / Navratilova, I. / van Aalten, D.M.F. / Tejero, T. / Merino, P. / Hurtado-Guerrero, R.
History
DepositionJun 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,3-beta-glucanosyltransferase GAS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4967
Polymers62,4261
Non-polymers1,0706
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-2 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.749, 70.591, 150.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1,3-beta-glucanosyltransferase GAS2 / Glycolipid-anchored surface protein 2


Mass: 62426.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: GAS2, YLR343W, L8300.5 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q06135, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-9PT / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[4-(3-quinolin-1-ium-1-ylpropyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol


Mass: 725.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H45N4O15
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3500, ammonium sulfate, BIS-Tris pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→75.21 Å / Num. obs: 37004 / % possible obs: 91.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 26
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 8.4 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W62

2w62


Resolution: 1.94→75.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.23 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21946 1091 3 %RANDOM
Rwork0.18866 ---
obs0.18961 35850 91.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.699 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--1.26 Å20 Å2
3----0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.94→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 72 318 3815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023597
X-RAY DIFFRACTIONr_bond_other_d0.0030.023264
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9824869
X-RAY DIFFRACTIONr_angle_other_deg1.0513.0067571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41524.709172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8761515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0112.4971719
X-RAY DIFFRACTIONr_mcbond_other1.012.4951718
X-RAY DIFFRACTIONr_mcangle_it1.7483.7252141
X-RAY DIFFRACTIONr_mcangle_other1.7483.7272142
X-RAY DIFFRACTIONr_scbond_it1.052.6921878
X-RAY DIFFRACTIONr_scbond_other1.0482.6921878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7813.9742727
X-RAY DIFFRACTIONr_long_range_B_refined4.5930.4644158
X-RAY DIFFRACTIONr_long_range_B_other4.5930.4754159
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.939→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 64 -
Rwork0.221 2164 -
obs--75.89 %
Refinement TLS params.Method: refined / Origin x: 19.5441 Å / Origin y: -8.0916 Å / Origin z: -19.9009 Å
111213212223313233
T0.1084 Å2-0.0134 Å2-0.017 Å2-0.0059 Å20.0113 Å2--0.0689 Å2
L1.0426 °2-0.1985 °20.1107 °2-0.2777 °2-0.1481 °2--0.1204 °2
S-0.0027 Å °0.0141 Å °0.1926 Å °-0.0286 Å °0.03 Å °0.0102 Å °0.0719 Å °-0.0223 Å °-0.0273 Å °

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