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

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Basic information

Entry
Database: PDB / ID: 1wds
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


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, conserved site / Beta-amylase active site 1. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-maltose / alpha-D-glucopyranose / Beta-amylase
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / rigid body refinement / Resolution: 1.64 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 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_atom_id / _struct_conn.ptnr1_label_comp_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
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
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,22611
Polymers55,9351
Non-polymers1,29110
Water14,214789
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.615, 84.615, 143.109
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-1277-

HOH

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Components

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


Mass: 55935.148 Da / Num. of mol.: 1 / Mutation: T342A
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)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.74 Å3/Da / Density % sol: 55.08 %
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: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Sep 3, 2003
RadiationMonochromator: carbon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.38→99 Å / Num. all: 121429 / Num. obs: 114150 / % possible obs: 94.01 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 10.2 Å2
Reflection shellResolution: 1.383→1.432 Å / % possible all: 73.25

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: rigid body refinement / Resolution: 1.64→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 788832.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6245 10.1 %RANDOM
Rwork0.171 ---
obs0.171 62116 85.2 %-
all-72874 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.9751 Å2 / ksol: 0.453573 e/Å3
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å22.34 Å20 Å2
2--1.88 Å20 Å2
3----3.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.64→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3927 0 76 789 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.592
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 1.64→1.74 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 916 9.8 %
Rwork0.254 8392 -
obs--77.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP10.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3CARBOHYDRATE.PARAM
X-RAY DIFFRACTION4ION.PARAM
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM

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