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- PDB-8in1: beta-glucosidase protein from Aplysia kurodai -

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Basic information

Entry
Database: PDB / ID: 8in1
Titlebeta-glucosidase protein from Aplysia kurodai
ComponentsBeta-Glucosidase
KeywordsHYDROLASE / glucosidase
Function / homology
Function and homology information


beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesAplysia kurodai (Kuroda's sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSun, X.M. / Ye, Y.X. / Kato, K. / Yu, J. / Yao, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H01754 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101083 Japan
CitationJournal: Elife / Year: 2023
Title: Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect aku BGL activity.
Authors: Sun, X. / Ye, Y. / Sakurai, N. / Wang, H. / Kato, K. / Yu, J. / Yuasa, K. / Tsuji, A. / Yao, M.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-Glucosidase
B: Beta-Glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,7698
Polymers225,1202
Non-polymers3,6496
Water1,72996
1
A: Beta-Glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5394
Polymers112,5601
Non-polymers1,9793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-Glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,2314
Polymers112,5601
Non-polymers1,6713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.669, 191.669, 112.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

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Protein / Non-polymers , 2 types, 98 molecules AB

#1: Protein Beta-Glucosidase


Mass: 112560.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aplysia kurodai (Kuroda's sea hare) / References: UniProt: A0A1V1FXL2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 878.823 Da / Num. of mol.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3-2/a3-b1_a4-c1_a6-e1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5, and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.65 Å / Num. obs: 64457 / % possible obs: 99.86 % / Redundancy: 10.7 % / Biso Wilson estimate: 42.39 Å2 / CC1/2: 0.995 / Net I/σ(I): 10.69
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.57 / Num. unique obs: 6309 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.65 Å / SU ML: 0.3747 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.7301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2195 3260 5.06 %
Rwork0.1831 61181 -
obs0.1849 64441 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.43 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15256 0 243 96 15595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004215939
X-RAY DIFFRACTIONf_angle_d0.65221667
X-RAY DIFFRACTIONf_chiral_restr0.04962308
X-RAY DIFFRACTIONf_plane_restr0.0052780
X-RAY DIFFRACTIONf_dihedral_angle_d16.75755759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.31651310.26062610X-RAY DIFFRACTION97.86
2.74-2.780.33911410.25892620X-RAY DIFFRACTION100
2.78-2.830.31911470.25822644X-RAY DIFFRACTION99.93
2.83-2.880.31511420.23962640X-RAY DIFFRACTION100
2.88-2.930.34011370.24822654X-RAY DIFFRACTION99.93
2.93-2.990.34051480.23772657X-RAY DIFFRACTION100
2.99-3.050.2941310.23012671X-RAY DIFFRACTION100
3.05-3.120.29261470.2352636X-RAY DIFFRACTION100
3.12-3.190.29771320.24312663X-RAY DIFFRACTION99.96
3.19-3.270.32441280.24832662X-RAY DIFFRACTION100
3.27-3.360.28961600.22592637X-RAY DIFFRACTION100
3.36-3.450.22841320.20722652X-RAY DIFFRACTION100
3.45-3.570.27411510.19462667X-RAY DIFFRACTION99.96
3.57-3.690.20991400.18662660X-RAY DIFFRACTION100
3.69-3.840.20311220.17372689X-RAY DIFFRACTION99.96
3.84-4.020.19761600.16262628X-RAY DIFFRACTION100
4.02-4.230.17331220.14722684X-RAY DIFFRACTION100
4.23-4.490.18041470.1392666X-RAY DIFFRACTION100
4.49-4.840.17331410.13332677X-RAY DIFFRACTION100
4.84-5.320.14921380.13722680X-RAY DIFFRACTION100
5.33-6.090.17961470.15552659X-RAY DIFFRACTION100
6.09-7.670.19691500.16412707X-RAY DIFFRACTION100
7.67-49.650.13381660.14852718X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 49.8074712124 Å / Origin y: 42.3099619723 Å / Origin z: 132.950302095 Å
111213212223313233
T0.291989847968 Å2-0.0155229129587 Å20.00949294577397 Å2-0.312889083708 Å20.0360660280598 Å2--0.271260798643 Å2
L0.353963475375 °2-0.0163776486598 °20.00931119813922 °2-0.359643628666 °20.0214583146943 °2--0.20296532236 °2
S0.00501649957162 Å °0.0548377163233 Å °0.0488374532895 Å °0.00159030945178 Å °-0.0256169239657 Å °-0.0507978188239 Å °-0.00556313144534 Å °0.0156500992069 Å °0.0261136790523 Å °
Refinement TLS groupSelection details: all

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