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- PDB-5o9p: Crystal structure of Gas2 in complex with compound 10 -

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Basic information

Entry
Database: PDB / ID: 5o9p
TitleCrystal structure of Gas2 in complex with compound 10
Components1,3-beta-glucanosyltransferase GAS2
KeywordsTRANSFERASE / Aspergillus fumigatus / AfGel4 / ScGas2 / transglycosylases / glucanosyltransferases / cell wall remodeling / fungal cell wall
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-9P8 / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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)63,1653
Polymers62,4261
Non-polymers7392
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.067, 70.953, 150.990
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-9P8 / (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-(pyridin-2-ylmethoxymethyl)-1,2,3-triazol-1-yl]oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol


Mass: 676.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H40N4O16
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
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: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→75.5 Å / Num. obs: 54873 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.7
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W62

2w62


Resolution: 1.75→75.5 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.675 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 1542 2.8 %RANDOM
Rwork0.21069 ---
obs0.21166 53117 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.772 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2--1.67 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.75→75.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 51 262 3776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023651
X-RAY DIFFRACTIONr_bond_other_d0.0020.023292
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9934944
X-RAY DIFFRACTIONr_angle_other_deg1.0393.0127642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7924.74173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04315592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9281515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214040
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
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_it0.9921.8121735
X-RAY DIFFRACTIONr_mcbond_other0.9881.8111734
X-RAY DIFFRACTIONr_mcangle_it1.7252.72160
X-RAY DIFFRACTIONr_mcangle_other1.7252.7012161
X-RAY DIFFRACTIONr_scbond_it1.0181.871916
X-RAY DIFFRACTIONr_scbond_other1.0171.871916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6912.7552785
X-RAY DIFFRACTIONr_long_range_B_refined3.55514.6084253
X-RAY DIFFRACTIONr_long_range_B_other3.55514.6124254
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 116 -
Rwork0.248 3899 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 5.5198 Å / Origin y: 8.1923 Å / Origin z: -20.0594 Å
111213212223313233
T0.0373 Å2-0.0034 Å20.0051 Å2-0.1282 Å2-0.023 Å2--0.0628 Å2
L0.4905 °2-0.1112 °2-0.0953 °2-0.2384 °20.1089 °2--0.1359 °2
S0.0079 Å °0.0223 Å °-0.1061 Å °-0.0035 Å °0.0171 Å °-0.0102 Å °-0.0541 Å °0.014 Å °-0.025 Å °

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