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- PDB-3axh: Crystal structure of isomaltase in complex with isomaltose -

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Basic information

Entry
Database: PDB / ID: 3axh
TitleCrystal structure of isomaltase in complex with isomaltose
ComponentsOligo-1,6-glucosidase IMA1
KeywordsHYDROLASE / (BETA/ALPHA)8-BARREL
Function / homology
Function and homology information


glucan 1,4-alpha-maltotriohydrolase activity / disaccharide catabolic process / sucrose alpha-glucosidase activity / sucrose catabolic process / oligo-1,6-glucosidase / oligo-1,6-glucosidase activity / maltose catabolic process / maltose alpha-glucosidase activity / alpha-amylase activity / mitochondrion
Similarity search - Function
Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Oligo-1,6-glucosidase IMA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYamamoto, K. / Miyake, H. / Kusunoki, M. / Osaki, S.
CitationJournal: J.Biosci.Bioeng. / Year: 2011
Title: Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae
Authors: Yamamoto, K. / Miyake, H. / Kusunoki, M. / Osaki, S.
History
DepositionApr 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _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 / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

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Assembly

Deposited unit
A: Oligo-1,6-glucosidase IMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0023
Polymers68,6191
Non-polymers3822
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.892, 114.736, 61.496
Angle α, β, γ (deg.)90.00, 90.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Oligo-1,6-glucosidase IMA1 / Alpha-glucosidase / Flocculent-specific protein 2 / Isomaltase 1


Mass: 68619.305 Da / Num. of mol.: 1 / Mutation: E277A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: D-346 / Gene: IMA1, FSP2, YGR287C / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P53051, oligo-1,6-glucosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 50mM HEPES pH 7.3, 0.2M lithium acetate, 21% (w/v) PEG 3350, 0.2M isomaltose , VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→24.38 Å / Num. all: 57876 / Num. obs: 56198 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AJ7

3aj7


Resolution: 1.8→24.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.932 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 3009 5.1 %RANDOM
Rwork0.168 ---
obs0.16927 56198 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.745 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 24 411 5266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225002
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9366780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25524.335263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30515830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1081525
X-RAY DIFFRACTIONr_chiral_restr0.0940.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023912
X-RAY DIFFRACTIONr_nbd_refined0.2050.22452
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23412
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2421
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.211
X-RAY DIFFRACTIONr_mcbond_it0.771.53012
X-RAY DIFFRACTIONr_mcangle_it1.24524729
X-RAY DIFFRACTIONr_scbond_it1.96332346
X-RAY DIFFRACTIONr_scangle_it3.14.52051
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 197 -
Rwork0.191 4003 -
obs--93.29 %

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