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- PDB-5wqs: Crystal structure of Apo Beta-Amylase from Sweet potato -

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Basic information

Entry
Database: PDB / ID: 5wqs
TitleCrystal structure of Apo Beta-Amylase from Sweet potato
ComponentsBeta-amylase
KeywordsHYDROLASE / Amylase / Apo / Sweet potato
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
ISOPROPYL ALCOHOL / Beta-amylase
Similarity search - Component
Biological speciesIpomoea batatas (sweet potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsVajravijayan, S. / Sergei, P. / Nandhagopal, N. / Gunasekaran, K.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Structural insights on starch hydrolysis by plant beta-amylase and its evolutionary relationship with bacterial enzymes
Authors: Vajravijayan, S. / Pletnev, S. / Mani, N. / Pletneva, N. / Nandhagopal, N. / Gunasekaran, K.
History
DepositionNov 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Structure summary
Category: entity / struct_ref_seq_dif / Item: _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0652
Polymers56,0051
Non-polymers601
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint2 kcal/mol
Surface area20060 Å2
Unit cell
Length a, b, c (Å)128.347, 128.347, 66.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 56005.297 Da / Num. of mol.: 1 / Fragment: UNP residues 2-499 / Source method: isolated from a natural source / Source: (natural) Ipomoea batatas (sweet potato) / References: UniProt: P10537, beta-amylase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1M Sodium acetate (pH 5.5), 0.05M Tris (pH 7.5), 0.01M NaCl, 2% Isoproponal, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2015
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→90.76 Å / Num. obs: 44300 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.093 / Net I/av σ(I): 20.541 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.976.60.6830.833197.8
1.97-2.057.40.5210.91199.5
2.05-2.147.90.3820.951199.8
2.14-2.2580.2880.973199.8
2.25-2.398.10.2130.982199.9
2.39-2.5880.1620.9881100
2.58-2.8480.1240.9921100
2.84-3.2580.0920.9951100
3.25-4.097.90.0720.9961100
4.09-307.50.0540.997199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FA2

1fa2


Resolution: 1.9→90.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.185 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 2213 5 %RANDOM
Rwork0.166 ---
obs0.1678 42046 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.67 Å2 / Biso mean: 33.203 Å2 / Biso min: 18.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.9→90.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3929 0 4 267 4200
Biso mean--43.66 37.39 -
Num. residues----496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194042
X-RAY DIFFRACTIONr_bond_other_d0.0020.023764
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9495484
X-RAY DIFFRACTIONr_angle_other_deg1.1238669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6135496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70924.67197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04915661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1741520
X-RAY DIFFRACTIONr_chiral_restr0.1490.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214639
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02949
X-RAY DIFFRACTIONr_mcbond_it2.7763.0351985
X-RAY DIFFRACTIONr_mcbond_other2.7763.0351986
X-RAY DIFFRACTIONr_mcangle_it3.6584.5272477
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 149 -
Rwork0.229 2840 -
all-2989 -
obs--92 %

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