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- PDB-1wdq: The role of an inner loop in the catalytic mechanism of soybean b... -

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Basic information

Entry
Database: PDB / ID: 1wdq
TitleThe role of an inner loop in the catalytic mechanism of soybean beta-amylase
ComponentsBeta-amylase
KeywordsHYDROLASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


amylopectin maltohydrolase activity / beta-amylase / beta-amylase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycoside hydrolase, family 14, conserved site / Glycosyl hydrolase family 14 / Beta-amylase active site 1. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Beta-amylase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.28 Å
AuthorsKang, Y.N. / Adachi, M. / Utsumi, S. / Mikami, B.
CitationJournal: Biochemistry / Year: 2005
Title: Structural analysis of threonine 342 mutants of soybean beta-amylase: role of a conformational change of the inner loop in the catalytic mechanism.
Authors: Kang, Y.N. / Tanabe, A. / Adachi, M. / Utsumi, S. / Mikami, B.
History
DepositionMay 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / 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_validate_chiral / struct_conn / 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_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _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_alt_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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1288
Polymers55,9631
Non-polymers1,1657
Water14,592810
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.989, 84.989, 144.023
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-847-

HOH

Detailsthe biological assembly is a monomer

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Components

#1: Protein Beta-amylase / / 1 / 4-alpha-D-glucan maltohydrolase


Mass: 55963.199 Da / Num. of mol.: 1 / Mutation: T342V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P10538, beta-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.71 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2003
RadiationMonochromator: rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. all: 229750 / Num. obs: 216884 / % possible obs: 94.4 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.12→1.16 Å / % possible all: 58.7

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.28→10 Å / Num. parameters: 43577 / Num. restraintsaints: 52029 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 7623 5.3 %RANDOM
all0.1173 144557 --
obs0.1347 135160 93.5 %-
Refine analyzeNum. disordered residues: 9 / Occupancy sum hydrogen: 3827 / Occupancy sum non hydrogen: 4815.5
Refinement stepCycle: LAST / Resolution: 1.28→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 72 810 4841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.087
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.079
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.096
LS refinement shellResolution: 1.28→1.3 Å
RfactorNum. reflection% reflection
Rwork0.201 --
obs-6566 93.88 %

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