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- PDB-8dl1: BoGH13ASus-E523Q from Bacteroides ovatus bound to maltoheptaose -

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Basic information

Entry
Database: PDB / ID: 8dl1
TitleBoGH13ASus-E523Q from Bacteroides ovatus bound to maltoheptaose
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
ACETATE ION / : / 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: 2.09 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

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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)350,80589
Polymers336,2194
Non-polymers14,58785
Water33,9941887
1
A: Alpha amylase, catalytic domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,25127
Polymers84,0551
Non-polymers4,19726
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)87,87726
Polymers84,0551
Non-polymers3,82325
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)87,79823
Polymers84,0551
Non-polymers3,74322
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)86,87913
Polymers84,0551
Non-polymers2,82412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.680, 128.640, 149.760
Angle α, β, γ (deg.)90.000, 105.370, 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: 84054.641 Da / Num. of mol.: 4 / Mutation: E523Q
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, 12 molecules

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


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4[DGlcpa1-6]DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}[(6+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D-glucopyranose-(1-4)]alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-6[DGlcpa1-4]DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_d6-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-6DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 10 types, 1960 molecules

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


Mass: 62.068 Da / Num. of mol.: 55
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#10: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#12: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#13: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H22O6 / Comment: precipitant*YM
#14: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#15: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na
#16: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#17: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1887 / 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: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% MPD, 12% PEG1000, 12% PEG3350, 0.1M Tris/Bicine pH 8.5, 0.08M ethylene glycols mix

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.09→47.93 Å / Num. obs: 212239 / % possible obs: 98.7 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 1.12 / Num. unique obs: 21205 / CC1/2: 0.467

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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: 2.09→47.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.481 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 10581 5 %RANDOM
Rwork0.1767 ---
obs0.179 201678 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.8 Å2 / Biso mean: 26.133 Å2 / Biso min: 6.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0.03 Å2
2--0.12 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.09→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22685 0 955 1887 25527
Biso mean--39.23 32.58 -
Num. residues----2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01324292
X-RAY DIFFRACTIONr_bond_other_d0.0020.01521282
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.69533037
X-RAY DIFFRACTIONr_angle_other_deg1.3221.61349220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47352834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41923.8221261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.465153572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3771576
X-RAY DIFFRACTIONr_chiral_restr0.0880.23299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025728
LS refinement shellResolution: 2.09→2.144 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 745 -
Rwork0.301 14956 -
all-15701 -
obs--99.22 %

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