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- PDB-7d9c: Alpha-glucosidase from Weissella cibaria BBK-1 bound with maltose -

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Basic information

Entry
Database: PDB / ID: 7d9c
TitleAlpha-glucosidase from Weissella cibaria BBK-1 bound with maltose
ComponentsAlpha-glycosidase
KeywordsHYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / alpha-maltose / beta-D-glucopyranose / alpha-D-glucopyranose
Function and homology information
Biological speciesWeissella confusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 13, 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)70,10813
Polymers68,3991
Non-polymers1,71012
Water11,061614
1
A: Alpha-glycosidase
hetero molecules

A: Alpha-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,21626
Polymers136,7972
Non-polymers3,41924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area10110 Å2
ΔGint-160 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.636, 115.636, 106.163
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-607-

SO4

21A-1144-

HOH

31A-1246-

HOH

41A-1305-

HOH

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Components

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Protein , 1 types, 1 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 confusa (bacteria) / Gene: C6P08_07940 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: alpha-glucosidase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
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
#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 623 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
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: Mar 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 152899 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 14.46 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 48.34
Reflection shellResolution: 1.36→1.41 Å / Num. unique obs: 15113 / Rpim(I) all: 0.358 / Rrim(I) all: 0.946

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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: 7D9B

7d9b


Resolution: 1.36→26.76 Å / SU ML: 0.1112 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.1479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1534 7635 5 %
Rwork0.1396 145208 -
obs0.1403 152843 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.34 Å2
Refinement stepCycle: LAST / Resolution: 1.36→26.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 101 614 5507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01555218
X-RAY DIFFRACTIONf_angle_d1.43017148
X-RAY DIFFRACTIONf_chiral_restr0.1106770
X-RAY DIFFRACTIONf_plane_restr0.0099926
X-RAY DIFFRACTIONf_dihedral_angle_d10.6853709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.21662470.20744779X-RAY DIFFRACTION99.66
1.38-1.390.19812510.19014758X-RAY DIFFRACTION100
1.39-1.410.2032540.18014803X-RAY DIFFRACTION100
1.41-1.430.20032390.16254799X-RAY DIFFRACTION100
1.43-1.450.17162550.15484792X-RAY DIFFRACTION100
1.45-1.470.15762520.14024769X-RAY DIFFRACTION100
1.47-1.490.16242510.13344797X-RAY DIFFRACTION100
1.49-1.510.15832560.12864789X-RAY DIFFRACTION100
1.51-1.530.15012310.12734803X-RAY DIFFRACTION100
1.53-1.560.14852690.12294809X-RAY DIFFRACTION100
1.56-1.590.14382630.1214800X-RAY DIFFRACTION100
1.59-1.610.13762550.11354782X-RAY DIFFRACTION100
1.61-1.650.13452470.11264791X-RAY DIFFRACTION100
1.65-1.680.1312520.11454820X-RAY DIFFRACTION100
1.68-1.720.1342400.11124827X-RAY DIFFRACTION100
1.72-1.760.13242680.11524806X-RAY DIFFRACTION100
1.76-1.80.13382560.11294815X-RAY DIFFRACTION100
1.8-1.850.13142340.1154857X-RAY DIFFRACTION100
1.85-1.90.12872670.11194806X-RAY DIFFRACTION100
1.9-1.960.13252570.11644826X-RAY DIFFRACTION100
1.96-2.030.14262520.12074839X-RAY DIFFRACTION100
2.03-2.120.13162530.12094852X-RAY DIFFRACTION99.96
2.12-2.210.12622500.12764863X-RAY DIFFRACTION100
2.21-2.330.15572530.13164849X-RAY DIFFRACTION100
2.33-2.470.15822640.13944881X-RAY DIFFRACTION100
2.47-2.670.15362590.15374890X-RAY DIFFRACTION99.96
2.67-2.930.17522570.16644896X-RAY DIFFRACTION99.98
2.93-3.360.17322660.16254939X-RAY DIFFRACTION100
3.36-4.230.1522660.13414997X-RAY DIFFRACTION99.98
4.23-26.760.16352710.16165174X-RAY DIFFRACTION99.07

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