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- PDB-2w61: Saccharomyces cerevisiae Gas2p apostructure (E176Q mutant) -

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Basic information

Entry
Database: PDB / ID: 2w61
TitleSaccharomyces cerevisiae Gas2p apostructure (E176Q mutant)
ComponentsGLYCOLIPID-ANCHORED SURFACE PROTEIN 2
KeywordsGLYCOPROTEIN / CELL MEMBRANE / FUNGAL CELL WALL / TRANSGLYCOSYLATION / GLUCAN / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN
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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1040 / Glucanosyltransferase / Glucanosyltransferase / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1040 / Glucanosyltransferase / Glucanosyltransferase / X8 domain / X8 domain / Possibly involved in carbohydrate binding / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsSchuettelkopf, A.W. / Hurtado-Guerrero, R. / van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Molecular Mechanisms of Yeast Cell Wall Glucan Remodeling.
Authors: Hurtado-Guerrero, R. / Schuttelkopf, A.W. / Mouyna, I. / Ibrahim, A.F.M. / Shepherd, S. / Fontaine, T. / Latge, J. / Van Aalten, D.M.F.
History
DepositionDec 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLYCOLIPID-ANCHORED SURFACE PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)62,4251
Polymers62,4251
Non-polymers00
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.883, 64.479, 152.038
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 GLYCOLIPID-ANCHORED SURFACE PROTEIN 2 / GAS2P


Mass: 62425.016 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: W303 / Plasmid: PPICZALPHA-BASED / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33
References: UniProt: Q06135, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 176 TO GLN
Has protein modificationY
Sequence detailsE176Q POINT MUTANT, MISSING RESIDUES WERE NOT MODELLED DUE TO LACKING ELECTRON DENSITY

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 100 MM SODIUM ACETATE PH 4.5; 5% ACETONE; 20% 1,4-BUTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→20 Å / Num. obs: 64209 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.12 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DERIVATIVE MODEL, NOT DEPOSITED

Resolution: 1.62→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.089 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 969 1.5 %RANDOM
Rwork0.175 ---
obs0.176 63183 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.62→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3732 0 0 677 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223861
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9585239
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.71424.684190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56515643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8461517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022994
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21788
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22686
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2497
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.52423
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26423809
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00531651
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9294.51424
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 62
Rwork0.229 4303
Refinement TLS params.Method: refined / Origin x: 4.1889 Å / Origin y: 24.6283 Å / Origin z: 19.3914 Å
111213212223313233
T-0.1556 Å20.0188 Å20.0153 Å2--0.1422 Å2-0.0032 Å2---0.1589 Å2
L0.6007 °20.2524 °20.0684 °2-0.8017 °20.1306 °2--0.5752 °2
S-0.0035 Å °0.0067 Å °0.0004 Å °-0.0488 Å °0.0143 Å °-0.0284 Å °0.0469 Å °0.0016 Å °-0.0107 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 64
2X-RAY DIFFRACTION1A71 - 359
3X-RAY DIFFRACTION1A364 - 506

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