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- PDB-2f6d: Structure of the complex of a glucoamylase from Saccharomycopsis ... -

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Basic information

Entry
Database: PDB / ID: 2f6d
TitleStructure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose
ComponentsGlucoamylase GLU1
KeywordsHYDROLASE / (alpha-alpha)6 barrel / protein-acarbose complex / sugar tongs
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / polysaccharide catabolic process
Similarity search - Function
Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
alpha-acarbose / PHOSPHATE ION / Glucoamylase GLU1
Similarity search - Component
Biological speciesSaccharomycopsis fibuligera (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSevcik, J. / Hostinova, E. / Solovicova, A. / Gasperik, J. / Dauter, Z. / Wilson, K.S.
Citation
Journal: Febs J. / Year: 2006
Title: Structure of the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on the catalytic domain.
Authors: Sevcik, J. / Hostinova, E. / Solovicova, A. / Gasperik, J. / Dauter, Z. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution.
Authors: Sevcik, J. / Solovicova, A. / Hostinova, E. / Gasperik, J. / Wilson, K.S. / Dauter, Z.
History
DepositionNov 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / diffrn_source / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucoamylase GLU1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0926
Polymers54,6601
Non-polymers1,4325
Water14,592810
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.580, 85.350, 97.510
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 Glucoamylase GLU1 / Glucan 1 / 4-alpha-glucosidase / 1 / 4-alpha-D-glucan glucohydrolase


Mass: 54659.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomycopsis fibuligera (fungus) / Strain: HUT 7212 / Gene: GLU1 / Plasmid: pET3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08017, glucan 1,4-alpha-glucosidase
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O

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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: 42.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 50 mM acetate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jul 9, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 1.6→10 Å / Num. obs: 59266 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.49 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.5
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1AYX

1ayx


Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.314 / SU ML: 0.046 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.117 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15958 3010 5.1 %RANDOM
Rwork0.11762 ---
all0.12 ---
obs0.11975 56255 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 95 810 4775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214058
X-RAY DIFFRACTIONr_bond_other_d0.0020.023365
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9655545
X-RAY DIFFRACTIONr_angle_other_deg1.04737887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335491
X-RAY DIFFRACTIONr_chiral_restr0.1590.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024611
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02824
X-RAY DIFFRACTIONr_nbd_refined0.2170.2984
X-RAY DIFFRACTIONr_nbd_other0.2480.24155
X-RAY DIFFRACTIONr_nbtor_other0.0850.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2611
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.299
X-RAY DIFFRACTIONr_mcbond_it0.9381.52443
X-RAY DIFFRACTIONr_mcangle_it1.53523928
X-RAY DIFFRACTIONr_scbond_it2.23731615
X-RAY DIFFRACTIONr_scangle_it3.3184.51617
X-RAY DIFFRACTIONr_rigid_bond_restr1.18424058
X-RAY DIFFRACTIONr_sphericity_free2.5932812
X-RAY DIFFRACTIONr_sphericity_bonded1.8223963
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.193 199
Rwork0.146 3705
obs-1788

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