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- PDB-5o9o: Crystal structure of ScGas2 in complex with compound 7. -

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Basic information

Entry
Database: PDB / ID: 5o9o
TitleCrystal structure of ScGas2 in complex with compound 7.
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-9PB / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDelso, I. / Valero-Gonzalez, J. / Fang, W. / Gomollon-Bel, F. / Castro-Lopez, J. / 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 1.2Oct 23, 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)63,4627
Polymers62,4261
Non-polymers1,0366
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint15 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.196, 70.714, 151.167
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-9PB / (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)-6-[4-(naphthalen-2-ylmethoxymethyl)-1,2,3-triazol-1-yl]-3,5-bis(oxidanyl)oxan-4-yl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-oxane-3,4,5-triol


Mass: 725.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H43N3O16
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 239 / 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: 42.76 %
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: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→70.71 Å / Num. obs: 43353 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W62

2w62


Resolution: 1.9→64.052 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.58
RfactorNum. reflection% reflection
Rfree0.2472 1226 2.86 %
Rwork0.1991 --
obs0.2005 42931 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→64.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 71 239 3723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093574
X-RAY DIFFRACTIONf_angle_d1.2284819
X-RAY DIFFRACTIONf_dihedral_angle_d14.2521320
X-RAY DIFFRACTIONf_chiral_restr0.053513
X-RAY DIFFRACTIONf_plane_restr0.006619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.42121180.39554486X-RAY DIFFRACTION97
1.9761-2.0660.3351270.25794599X-RAY DIFFRACTION100
2.066-2.17490.26761520.24724522X-RAY DIFFRACTION98
2.1749-2.31120.31421110.25454515X-RAY DIFFRACTION98
2.3112-2.48970.22931420.19694639X-RAY DIFFRACTION100
2.4897-2.74020.26761520.20114627X-RAY DIFFRACTION100
2.7402-3.13670.2391420.19184687X-RAY DIFFRACTION100
3.1367-3.95190.21161360.1694710X-RAY DIFFRACTION100
3.9519-64.08870.22291460.16524920X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.9981 Å / Origin y: 8.6042 Å / Origin z: 19.8731 Å
111213212223313233
T0.1875 Å20.0331 Å20.0017 Å2-0.1553 Å20.0397 Å2--0.1891 Å2
L1.6078 °20.1032 °2-0.3566 °2-0.7346 °2-0.3068 °2--1.1799 °2
S-0.0178 Å °-0.1307 Å °-0.2058 Å °0.0515 Å °0.0655 Å °0.0338 Å °-0.0737 Å °-0.0095 Å °-0.0196 Å °
Refinement TLS groupSelection details: (chain A and resseq 29:489)

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