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

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Basic information

Entry
Database: PDB / ID: 1wdp
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 / amylopectin maltohydrolase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase, family 14B, plant / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.27 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)56,6388
Polymers55,9651
Non-polymers6727
Water15,529862
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.888, 84.888, 143.397
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-1169-

HOH

21A-1252-

HOH

Detailsthe biological assembly is a monomer

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Components

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


Mass: 55965.172 Da / Num. of mol.: 1
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
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: BL41XU / Wavelength: 0.71 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Nov 29, 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: 1.25→50 Å / Num. all: 165296 / Num. obs: 163644 / % possible obs: 99 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.25→1.29 Å / % possible all: 100

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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: 1.27→10 Å / Num. parameters: 43836 / Num. restraintsaints: 52107 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 7796 5.3 %RANDOM
all0.1179 147861 --
obs0.134 139140 94.1 %-
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 3825 / Occupancy sum non hydrogen: 4831
Refinement stepCycle: LAST / Resolution: 1.27→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 35 862 4870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0281
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.078
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.082
LS refinement shellResolution: 1.27→1.3 Å
RfactorNum. reflection% reflection
Rwork0.177 --
obs-10059 95.05 %

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