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- PDB-7dch: Alpha-glucosidase from Weissella cibaria BBK-1 bound with acarbose -

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Basic information

Entry
Database: PDB / ID: 7dch
TitleAlpha-glucosidase from Weissella cibaria BBK-1 bound with acarbose
ComponentsAlpha-glycosidase
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: 1.692 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,14312
Polymers68,3991
Non-polymers1,74511
Water9,656536
1
A: Alpha-glycosidase
hetero molecules

A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,28624
Polymers136,7972
Non-polymers3,48922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area12400 Å2
ΔGint-149 kcal/mol
Surface area43360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.992, 116.992, 107.167
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-605-

SO4

21A-986-

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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 546 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.: 1 / 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: isolated from a genetically manipulated source
Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
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: 1.69→50 Å / Num. obs: 76028 / % possible obs: 91.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.31 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Net I/σ(I): 21.244
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.2 % / Num. unique obs: 15816 / Rpim(I) all: 0.416

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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: 1.692→27.755 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.203 3790 -
Rwork0.1769 --
obs-75762 91.17 %
Displacement parametersBiso mean: 26.25 Å2
Refinement stepCycle: LAST / Resolution: 1.692→27.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 105 536 5455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915199
X-RAY DIFFRACTIONf_angle_d1.08057108
X-RAY DIFFRACTIONf_chiral_restr0.0668759
X-RAY DIFFRACTIONf_plane_restr0.0072920
X-RAY DIFFRACTIONf_dihedral_angle_d18.53791909
LS refinement shellResolution: 1.692→1.7136 Å
RfactorNum. reflection% reflection
Rfree0.3169 150 -
Rwork0.2416 --
obs-3005 99 %

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