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- PDB-2w62: Saccharomyces cerevisiae Gas2p in complex with laminaripentaose -

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Basic information

Entry
Database: PDB / ID: 2w62
TitleSaccharomyces cerevisiae Gas2p in complex with laminaripentaose
ComponentsGLYCOLIPID-ANCHORED SURFACE PROTEIN 2
KeywordsTRANSFERASE / GLYCOPROTEIN / 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 / ascospore wall assembly / fungal-type cell wall organization / 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
1,4-BUTANEDIOL / 1,3-beta-glucanosyltransferase GAS2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 17, 2011Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Refinement description / Structure summary
Revision 1.3Feb 8, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: GLYCOLIPID-ANCHORED SURFACE PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1744
Polymers62,4261
Non-polymers1,7483
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.039, 70.841, 149.149
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: 62426.000 Da / Num. of mol.: 1
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: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMISSING 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: 1.85→20 Å / Num. obs: 45921 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DERIVATIVE MODEL, NOT DEPOSITED

Resolution: 1.85→23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.048 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 555 1.2 %RANDOM
Rwork0.183 ---
obs0.184 45304 99.5 %-
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: 42.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--0.21 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 118 313 3905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223721
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.0335059
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8785443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92724.746177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92515602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2421515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212779
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8391.52187
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46823534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.26931534
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4414.51519
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 48
Rwork0.201 3182
Refinement TLS params.Method: refined / Origin x: 5.4387 Å / Origin y: 27.3502 Å / Origin z: 19.5125 Å
111213212223313233
T-0.1586 Å20.048 Å20.0155 Å2--0.1446 Å2-0.0122 Å2---0.2062 Å2
L1.9553 °20.3959 °20.4071 °2-1.3753 °20.5677 °2--1.2669 °2
S0.0147 Å °-0.0961 Å °0.1689 Å °0.0367 Å °0.0083 Å °-0.0971 Å °0.119 Å °0.0141 Å °-0.023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 64
2X-RAY DIFFRACTION1A75 - 355
3X-RAY DIFFRACTION1A363 - 404
4X-RAY DIFFRACTION1A409 - 482
5X-RAY DIFFRACTION1A489
6X-RAY DIFFRACTION1A1490 - 1491

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