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- PDB-7d9b: Crystal structure of alpha-glucosidase -

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Basic information

Entry
Database: PDB / ID: 7d9b
TitleCrystal structure of alpha-glucosidase
ComponentsAlpha-glycosidase
KeywordsHYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesWeissella cibaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 12, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,29510
Polymers68,4001
Non-polymers8969
Water8,683482
1
A: Alpha-glycosidase
hetero molecules

A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,59120
Polymers136,7992
Non-polymers1,79218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area9600 Å2
ΔGint-133 kcal/mol
Surface area42150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.503, 116.503, 106.638
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-1006-

SO4

21A-1404-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-glycosidase


Mass: 68399.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella cibaria (bacteria) / Gene: C6P22_07685 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 491 molecules

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


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


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


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


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 53.53 %
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: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 99818 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 21.91 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.048 / Net I/σ(I): 23.18
Reflection shellResolution: 1.58→1.69 Å / Num. unique obs: 36945 / Rpim(I) all: 0.019 / Rrim(I) all: 0.047

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Processing

Software
NameVersionClassification
REFMAC7.0.069refinement
PHENIX1.17_3644refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVI

1gvi


Resolution: 1.58→32.31 Å / SU ML: 0.1378 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.8107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1763 4979 4.99 %
Rwork0.1454 94792 -
obs0.1469 99771 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 1.58→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 51 482 5323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345114
X-RAY DIFFRACTIONf_angle_d1.20256981
X-RAY DIFFRACTIONf_chiral_restr0.0762738
X-RAY DIFFRACTIONf_plane_restr0.0085912
X-RAY DIFFRACTIONf_dihedral_angle_d16.6248694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.25871520.21782828X-RAY DIFFRACTION90
1.6-1.620.23351750.18683040X-RAY DIFFRACTION97.25
1.62-1.640.21551570.1613116X-RAY DIFFRACTION99.24
1.64-1.660.21551790.14213095X-RAY DIFFRACTION99.88
1.66-1.680.20011580.13273129X-RAY DIFFRACTION100
1.68-1.70.18751510.12623172X-RAY DIFFRACTION100
1.7-1.730.1771580.1233157X-RAY DIFFRACTION100
1.73-1.750.1871700.12493139X-RAY DIFFRACTION99.97
1.75-1.780.18561680.12053118X-RAY DIFFRACTION100
1.78-1.810.16371710.11893166X-RAY DIFFRACTION100
1.81-1.840.1951650.12753142X-RAY DIFFRACTION100
1.84-1.870.18051650.12193170X-RAY DIFFRACTION100
1.87-1.910.16871640.11913147X-RAY DIFFRACTION100
1.91-1.950.16741650.11693133X-RAY DIFFRACTION100
1.95-1.990.16381850.12163139X-RAY DIFFRACTION100
1.99-2.040.16971540.12233168X-RAY DIFFRACTION100
2.04-2.090.14851830.12513156X-RAY DIFFRACTION100
2.09-2.140.17771710.1273142X-RAY DIFFRACTION100
2.14-2.210.16651730.1363179X-RAY DIFFRACTION100
2.21-2.280.17711560.13353167X-RAY DIFFRACTION100
2.28-2.360.17381820.13463163X-RAY DIFFRACTION100
2.36-2.450.15931690.13613191X-RAY DIFFRACTION100
2.45-2.570.18431720.14733167X-RAY DIFFRACTION99.97
2.57-2.70.15691510.15163223X-RAY DIFFRACTION99.97
2.7-2.870.18071690.15053208X-RAY DIFFRACTION99.85
2.87-3.090.1841400.16043238X-RAY DIFFRACTION99.79
3.09-3.40.17191650.16143214X-RAY DIFFRACTION99.76
3.4-3.90.16441630.14473247X-RAY DIFFRACTION99.27
3.9-4.90.16561750.14333240X-RAY DIFFRACTION98.56
4.91-32.310.20741730.17913398X-RAY DIFFRACTION97.84

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