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- PDB-7ehh: Crystal structure of alpha-glucosidase from Weissella cibaria BKK... -

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Basic information

Entry
Database: PDB / ID: 7ehh
TitleCrystal structure of alpha-glucosidase from Weissella cibaria BKK1 in complex with maltose
Componentsalpha-glucosidase
KeywordsHYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism / CARBOHYDRATE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesWeissella cibaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 29, 2021Deposition 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-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,02414
Polymers68,3991
Non-polymers1,62613
Water7,728429
1
A: alpha-glucosidase
hetero molecules

A: alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,04828
Polymers136,7972
Non-polymers3,25126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area11600 Å2
ΔGint-148 kcal/mol
Surface area42690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.031, 116.031, 106.450
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-706-

SO4

21A-1134-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein alpha-glucosidase


Mass: 68398.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Weissella cibaria (bacteria) / 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 / alpha-maltose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 441 molecules

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


Mass: 195.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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
#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.: 429 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. AUTHORS 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 67707 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.72 Å2 / Rpim(I) all: 0.089 / Rrim(I) all: 0.229 / Net I/σ(I): 19.51
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 6686 / CC1/2: 0.249

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D9B

7d9b


Resolution: 2→32.18 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.175
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1918 2449 5 %
Rwork0.1593 46526 -
obs0.1609 48975 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.56 Å2
Refinement stepCycle: LAST / Resolution: 2→32.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 96 429 5290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915154
X-RAY DIFFRACTIONf_angle_d1.21047053
X-RAY DIFFRACTIONf_chiral_restr0.0789758
X-RAY DIFFRACTIONf_plane_restr0.008910
X-RAY DIFFRACTIONf_dihedral_angle_d17.74331884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24221390.16482647X-RAY DIFFRACTION97.07
2.05-2.090.18271410.15172680X-RAY DIFFRACTION100
2.09-2.140.21911430.14992705X-RAY DIFFRACTION100
2.14-2.190.21661430.1542735X-RAY DIFFRACTION100
2.19-2.250.2091420.1472697X-RAY DIFFRACTION100
2.25-2.320.20991450.14682738X-RAY DIFFRACTION100
2.32-2.390.21121420.14912697X-RAY DIFFRACTION99.93
2.39-2.480.19761440.15272749X-RAY DIFFRACTION99.93
2.48-2.580.20371430.15782719X-RAY DIFFRACTION99.86
2.58-2.690.18081440.15422720X-RAY DIFFRACTION99.83
2.69-2.840.22721440.15772744X-RAY DIFFRACTION99.86
2.84-3.010.22431440.17482731X-RAY DIFFRACTION99.79
3.01-3.250.19311440.1642741X-RAY DIFFRACTION99.28
3.25-3.570.15671460.15672766X-RAY DIFFRACTION99.45
3.57-4.090.17041460.14252777X-RAY DIFFRACTION99.46
4.09-5.150.14291470.14772806X-RAY DIFFRACTION98.89
5.15-32.180.22431520.20222874X-RAY DIFFRACTION96.34

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