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- PDB-7dcg: Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltotriose -

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Basic information

Entry
Database: PDB / ID: 7dcg
TitleAlpha-glucosidase from Weissella cibaria BBK-1 bound with maltotriose
ComponentsAlpha-glycosidase
KeywordsHYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism / alpha-glucosidase
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / alpha-maltotriose
Function and homology information
Biological speciesWeissella cibaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsKrusong, K. / Wangpaiboon, K. / Kim, S. / Mori, T. / Hakoshima, T.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other government Thailand
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: A GH13 alpha-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides.
Authors: Wangpaiboon, K. / Laohawuttichai, P. / Kim, S.Y. / Mori, T. / Nakapong, S. / Pichyangkura, R. / Pongsawasdi, P. / Hakoshima, T. / Krusong, K.
History
DepositionOct 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,18614
Polymers68,3991
Non-polymers1,78813
Water10,106561
1
A: Alpha-glycosidase
hetero molecules

A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,37328
Polymers136,7972
Non-polymers3,57526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area12740 Å2
ΔGint-145 kcal/mol
Surface area42690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.375, 116.375, 107.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-1308-

SO4

21A-1818-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Alpha-glycosidase


Mass: 68398.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella cibaria (bacteria) / Gene: C6P12_07850, C6P22_07685 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: alpha-glucosidase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 573 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS MG_256496 FOR THE PROTEIN.

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, dioxane, MES

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 109716 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.92 Å2 / Rpim(I) all: 0.045 / Net I/σ(I): 15.3
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 6.5 % / Num. unique obs: 10808 / Rpim(I) all: 0.602

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Processing

Software
NameVersionClassification
REFMAC7.0.069refinement
PHENIX1.17_3644refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D9B

7d9b


Resolution: 1.53→26.02 Å / SU ML: 0.1168 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.5091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1602 5399 4.92 %
Rwork0.1283 104264 -
obs0.1299 109663 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.79 Å2
Refinement stepCycle: LAST / Resolution: 1.53→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 107 561 5458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01785214
X-RAY DIFFRACTIONf_angle_d1.39977137
X-RAY DIFFRACTIONf_chiral_restr0.0961764
X-RAY DIFFRACTIONf_plane_restr0.0101923
X-RAY DIFFRACTIONf_dihedral_angle_d13.473741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.19481550.15243314X-RAY DIFFRACTION95.8
1.55-1.570.23731880.15043420X-RAY DIFFRACTION100
1.57-1.590.18381890.14613411X-RAY DIFFRACTION100
1.59-1.610.22721680.14153452X-RAY DIFFRACTION100
1.61-1.630.20861550.13293454X-RAY DIFFRACTION100
1.63-1.650.20031720.12783459X-RAY DIFFRACTION100
1.65-1.680.18781930.12453415X-RAY DIFFRACTION100
1.68-1.70.19761930.1283449X-RAY DIFFRACTION100
1.7-1.730.16361680.11753445X-RAY DIFFRACTION100
1.73-1.760.16491730.10663455X-RAY DIFFRACTION99.97
1.76-1.790.1511780.0983431X-RAY DIFFRACTION99.97
1.79-1.820.14461890.09583484X-RAY DIFFRACTION100
1.82-1.850.15791560.09783443X-RAY DIFFRACTION100
1.85-1.890.13341850.09743451X-RAY DIFFRACTION99.97
1.89-1.930.15121760.10063460X-RAY DIFFRACTION100
1.93-1.980.13011800.10213465X-RAY DIFFRACTION100
1.98-2.030.14591970.10563454X-RAY DIFFRACTION100
2.03-2.080.14271830.10363464X-RAY DIFFRACTION99.92
2.08-2.140.16951670.11133479X-RAY DIFFRACTION99.97
2.14-2.210.16222040.11533419X-RAY DIFFRACTION99.94
2.21-2.290.14691770.1193504X-RAY DIFFRACTION99.97
2.29-2.380.14471670.11943487X-RAY DIFFRACTION100
2.38-2.490.16021790.12363515X-RAY DIFFRACTION99.97
2.49-2.620.15921880.13223467X-RAY DIFFRACTION100
2.62-2.790.15311810.13893517X-RAY DIFFRACTION100
2.79-30.14381700.14343536X-RAY DIFFRACTION100
3-3.30.17541630.14893559X-RAY DIFFRACTION99.92
3.3-3.780.16641730.1353557X-RAY DIFFRACTION99.81
3.78-4.760.14711890.12093598X-RAY DIFFRACTION99.89
4.76-26.020.17052430.16743700X-RAY DIFFRACTION98.95

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