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- PDB-8dl2: BoGH13ASus from Bacteroides ovatus bound to acarbose -

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Basic information

Entry
Database: PDB / ID: 8dl2
TitleBoGH13ASus from Bacteroides ovatus bound to acarbose
ComponentsAlpha amylase, catalytic domain protein
KeywordsHYDROLASE / alpha-amylase / starch / GH13 / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / ACETATE ION / alpha-D-glucopyranose / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha amylase, catalytic domain protein
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsBrown, H.A. / DeVeaux, A.L. / Koropatkin, N.M.
Funding support United States, 2items
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)AT011278 United States
CitationJournal: Cell.Mol.Life Sci. / Year: 2023
Title: BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
Authors: Brown, H.A. / DeVeaux, A.L. / Juliano, B.R. / Photenhauer, A.L. / Boulinguiez, M. / Bornschein, R.E. / Wawrzak, Z. / Ruotolo, B.T. / Terrapon, N. / Koropatkin, N.M.
History
DepositionJul 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Apr 10, 2024Group: Atomic model / Derived calculations / Category: atom_site / struct_conn / Item: _atom_site.label_alt_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha amylase, catalytic domain protein
B: Alpha amylase, catalytic domain protein
C: Alpha amylase, catalytic domain protein
D: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,94143
Polymers336,2234
Non-polymers10,71839
Water41,0022276
1
A: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,95511
Polymers84,0561
Non-polymers2,90010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,02113
Polymers84,0561
Non-polymers2,96612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67310
Polymers84,0561
Non-polymers2,6179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2919
Polymers84,0561
Non-polymers2,2358
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.080, 125.310, 150.780
Angle α, β, γ (deg.)90.000, 102.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha amylase, catalytic domain protein


Mass: 84055.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Strain: ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153
Gene: BACOVA_03514,Bovatus_03803 / Production host: Escherichia coli (E. coli) / References: UniProt: A7M087

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Sugars , 7 types, 15 molecules

#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)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: 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, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-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, Oligosaccharide / Class: Inhibitor / Mass: 969.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


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
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-glucopyranose-(1-4)-4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl) ...alpha-D-glucopyranose-(1-4)-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, Oligosaccharide / Class: Inhibitor / Mass: 807.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][non_ch_ring]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 9 types, 2300 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#13: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#14: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#15: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#16: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2276 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 mM acarbose, 0.1 M HEPES/MOPS, pH 7.5, 0.12 monosaccharides mix (Glc, Man, Gal, Fuc, Xyl, GlcNAc), 20% ethylene glycol, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.99→38.6 Å / Num. obs: 244819 / % possible obs: 98.5 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.6
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 1.05 / Num. unique obs: 23974 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DGE

8dge


Resolution: 1.99→38.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.533 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 12246 5 %RANDOM
Rwork0.1754 ---
obs0.1776 232585 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.17 Å2 / Biso mean: 24.256 Å2 / Biso min: 5.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.06 Å2
2---0.09 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.99→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22732 0 706 2276 25714
Biso mean--32.36 31.67 -
Num. residues----2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01324192
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521155
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6833010
X-RAY DIFFRACTIONr_angle_other_deg1.3451.60448912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41152861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89923.7721270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.194153598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4981575
X-RAY DIFFRACTIONr_chiral_restr0.0750.23275
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0227350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025774
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 913 -
Rwork0.308 16778 -
all-17691 -
obs--96.49 %

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