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- PDB-5wqu: Crystal structure of Sweet Potato Beta-Amylase complexed with Mal... -

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Basic information

Entry
Database: PDB / ID: 5wqu
TitleCrystal structure of Sweet Potato Beta-Amylase complexed with Maltotetraose
ComponentsBeta-amylase
KeywordsHYDROLASE / Amylase / maltotetraose / 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
alpha-maltotetraose / Beta-amylase
Similarity search - Component
Biological speciesIpomoea batatas (sweet potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_close_contact / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6732
Polymers56,0061
Non-polymers6671
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-20 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.547, 128.547, 66.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 56006.242 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: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 49.63 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1M Na Acetate (pH 5.5), 0.05M Tris (pH 7.5), 0.01M NaCl, 2% Isopropanol and 18% PEG 4000
PH range: 5.5-7.5

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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: Jan 5, 2016
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→90.9 Å / Num. obs: 19723 / % possible obs: 98.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.144 / Net I/av σ(I): 12.593 / Net I/σ(I): 6.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.594.50.7220.687199.5
2.59-2.694.50.5690.806199.4
2.69-2.824.60.4210.886199.3
2.82-2.964.70.3150.93199.3
2.96-3.154.70.2270.957199
3.15-3.394.70.1630.981199
3.39-3.734.70.1250.98198.7
3.73-4.274.60.1060.983198.6
4.27-5.384.60.0990.984198.1
5.38-504.40.1080.977196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wqs

5wqs


Resolution: 2.49→90.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.889 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24504 956 4.9 %RANDOM
Rwork0.16648 ---
obs0.1704 18743 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.456 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.49→90.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 45 154 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194064
X-RAY DIFFRACTIONr_bond_other_d0.0020.023758
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.965516
X-RAY DIFFRACTIONr_angle_other_deg1.03338667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.824.67197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2815657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7831520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214610
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02946
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0324.1581973
X-RAY DIFFRACTIONr_mcbond_other3.0274.1571972
X-RAY DIFFRACTIONr_mcangle_it4.6116.2292461
X-RAY DIFFRACTIONr_mcangle_other4.616.2322462
X-RAY DIFFRACTIONr_scbond_it3.7094.4652091
X-RAY DIFFRACTIONr_scbond_other3.7084.4652091
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8056.553056
X-RAY DIFFRACTIONr_long_range_B_refined7.49448.1834618
X-RAY DIFFRACTIONr_long_range_B_other7.49448.1684608
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.491→2.556 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 47 -
Rwork0.234 1376 -
obs--98.21 %

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