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- PDB-9bs5: Bacteroides ovatus GH97C Sus -

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Basic information

Entry
Database: PDB / ID: 9bs5
TitleBacteroides ovatus GH97C Sus
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / glycoside hydrolase family 97 / GH97 / Bacteroides ovatus / SusB
Function / homology
Function and homology information


carbohydrate binding / hydrolase activity
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / : / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Glycoside hydrolase-type carbohydrate-binding / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-glucosidase
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsBrown, H.A. / Koropatkin, N.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118475 United States
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)F32-AT011278 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK125445 United States
CitationJournal: Mbio / Year: 2024
Title: Acarbose impairs gut Bacteroides growth by targeting intracellular glucosidases.
Authors: Brown, H.A. / Morris, A.L. / Pudlo, N.A. / Hopkins, A.E. / Martens, E.C. / Golob, J.L. / Koropatkin, N.M.
History
DepositionMay 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,03827
Polymers165,6102
Non-polymers2,42825
Water26,8781492
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.855, 116.528, 144.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Alpha-glucosidase / Glycoside hydrolase family 97 protein


Mass: 82804.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: DHW41_19285, DWX70_08180, DWY24_08950, DYI28_22155, F3D51_05285, F3F51_00675, R4E93_19165
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y4Q1A2
#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


Type: oligosaccharide / Mass: 483.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 1515 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1492 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen condition that included 100 mM NaHEPES/MOPS pH 7.5 (Thermo), 100 mM amino acids and 36% precipitant mix 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.46→51.26 Å / Num. obs: 312566 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 1.46→1.48 Å / Num. unique obs: 10323 / CC1/2: 0.524 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→51.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.651 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 15899 5.1 %RANDOM
Rwork0.204 ---
obs0.205 296665 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.143 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.55 Å2
Refinement stepCycle: 1 / Resolution: 1.46→51.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11035 0 157 1492 12684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01311463
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610463
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.65215522
X-RAY DIFFRACTIONr_angle_other_deg1.2311.58524126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50851373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62623.553608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.595151872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7391546
X-RAY DIFFRACTIONr_chiral_restr0.0560.21485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022707
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6281.1955504
X-RAY DIFFRACTIONr_mcbond_other0.6281.1965505
X-RAY DIFFRACTIONr_mcangle_it0.8851.7956873
X-RAY DIFFRACTIONr_mcangle_other0.8851.7956874
X-RAY DIFFRACTIONr_scbond_it0.7761.3165959
X-RAY DIFFRACTIONr_scbond_other0.7761.3165960
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0081.9128650
X-RAY DIFFRACTIONr_long_range_B_refined2.815.65613307
X-RAY DIFFRACTIONr_long_range_B_other2.815.65613308
X-RAY DIFFRACTIONr_rigid_bond_restr2.707321926
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 1135 -
Rwork0.447 21781 -
obs--99.89 %
Refinement TLS params.

L11: 0 °2 / S11: 0.0004 Å ° / S21: -0.0002 Å ° / S33: -0.0005 Å ° / T11: 0.0467 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S12 (Å °)S13 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0001-00.0005-0.00020.00010.00040.00020.00020.00080.00080.0007-00.00050.0389-0.00080.00156.29686.183620.8981
2-000.0001-0.00010.0002-0.0005-0.00010.00010.0002-0.00090.001-0.0008-0.00040.038-0.0010.00056.166535.7223-20.7936
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 726
2X-RAY DIFFRACTION2B22 - 801

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