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- PDB-5o9r: Crystal structure of ScGas2 in complex with compound 9 -

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Basic information

Entry
Database: PDB / ID: 5o9r
TitleCrystal structure of ScGas2 in complex with compound 9
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-9PK / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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)64,36314
Polymers62,4261
Non-polymers1,93713
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint2 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.200, 71.200, 150.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 340 molecules

#3: Chemical ChemComp-9PK / (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-(thiophen-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: 681.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39N3O16S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 42.88 %
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: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→150.44 Å / Num. obs: 60003 / % possible obs: 99.6 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 3 / % possible all: 97.7

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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: 1.7→150.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.928 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21193 1831 3.1 %RANDOM
Rwork0.19539 ---
obs0.19592 58100 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2--1.54 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.7→150.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 126 328 3872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023616
X-RAY DIFFRACTIONr_bond_other_d0.0020.023293
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9944885
X-RAY DIFFRACTIONr_angle_other_deg0.9333.0067628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68124.675169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2031515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
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_it0.5251.8581711
X-RAY DIFFRACTIONr_mcbond_other0.5251.8571710
X-RAY DIFFRACTIONr_mcangle_it0.9772.7752130
X-RAY DIFFRACTIONr_mcangle_other0.9772.7772131
X-RAY DIFFRACTIONr_scbond_it0.4431.9571905
X-RAY DIFFRACTIONr_scbond_other0.4421.9421897
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7832.8722744
X-RAY DIFFRACTIONr_long_range_B_refined3.45615.5264281
X-RAY DIFFRACTIONr_long_range_B_other3.45615.5284282
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 100 -
Rwork0.267 4066 -
obs--94.64 %
Refinement TLS params.Method: refined / Origin x: -5.4868 Å / Origin y: 8.0846 Å / Origin z: 19.731 Å
111213212223313233
T0.0538 Å20.0025 Å20.0029 Å2-0.0175 Å20.017 Å2--0.0502 Å2
L0.618 °20.1562 °2-0.1271 °2-0.2795 °2-0.1454 °2--0.2043 °2
S0.0054 Å °-0.0291 Å °-0.1098 Å °-0.003 Å °0.0231 Å °0.0177 Å °-0.0685 Å °-0.0078 Å °-0.0286 Å °

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