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- PDB-5z9s: Functional and Structural Characterization of a beta-Glucosidase ... -

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Basic information

Entry
Database: PDB / ID: 5z9s
TitleFunctional and Structural Characterization of a beta-Glucosidase Involved in Saponin Metabolism from Intestinal Bacteria
ComponentsGlycosyl hydrolase family 3 protein
KeywordsHYDROLASE / Saponins / glucosidase / biotransformation / Bifidobacterium longum
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-glucosidase / Beta-glucosidase-like glycosidase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYan, S. / Wei, P.C. / Li, J.R.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470388 China
National Natural Science Foundation of China31470738 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Functional and structural characterization of a beta-glucosidase involved in saponin metabolism from intestinal bacteria.
Authors: Yan, S. / Wei, P.C. / Chen, Q. / Chen, X. / Wang, S.C. / Li, J.R. / Gao, C.
History
DepositionFeb 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 3 protein
B: Glycosyl hydrolase family 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,3244
Polymers171,9632
Non-polymers3602
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-12 kcal/mol
Surface area49630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.954, 134.419, 90.285
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyl hydrolase family 3 protein / beta-Glucosidase / BlBG3


Mass: 85981.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: HMPREF3231_00214 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A133LV16, UniProt: F8ATF7*PLUS
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: sodium formate, BICINE, polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→47.85 Å / Num. obs: 70856 / % possible obs: 99 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6276 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U48

3u48


Resolution: 2.3→47.85 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2418 2000 2.82 %
Rwork0.224 --
obs0.2245 70848 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11598 0 24 476 12098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311852
X-RAY DIFFRACTIONf_angle_d0.73216134
X-RAY DIFFRACTIONf_dihedral_angle_d16.0777050
X-RAY DIFFRACTIONf_chiral_restr0.0481837
X-RAY DIFFRACTIONf_plane_restr0.0042121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2997-2.35720.33481210.29484190X-RAY DIFFRACTION84
2.3572-2.42090.29371370.28754698X-RAY DIFFRACTION94
2.4209-2.49210.29641430.28684931X-RAY DIFFRACTION98
2.4921-2.57260.28481440.27234958X-RAY DIFFRACTION100
2.5726-2.66450.25511450.26554980X-RAY DIFFRACTION100
2.6645-2.77120.30631440.25514984X-RAY DIFFRACTION100
2.7712-2.89730.26421460.25365011X-RAY DIFFRACTION100
2.8973-3.050.2851440.25264962X-RAY DIFFRACTION100
3.05-3.24110.27981460.24555007X-RAY DIFFRACTION100
3.2411-3.49130.26011460.22875023X-RAY DIFFRACTION100
3.4913-3.84250.2361450.20835001X-RAY DIFFRACTION100
3.8425-4.39810.19581450.18564993X-RAY DIFFRACTION100
4.3981-5.53990.18231460.18695040X-RAY DIFFRACTION100
5.5399-47.85990.20751480.18625070X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 71.2562 Å / Origin y: -22.1078 Å / Origin z: 22.7085 Å
111213212223313233
T0.2703 Å2-0.0056 Å2-0.0065 Å2-0.2386 Å2-0.0097 Å2--0.3052 Å2
L0.591 °20.0609 °2-0.0914 °2-0.3412 °20.0159 °2--0.9569 °2
S-0.0217 Å °-0.002 Å °0.0092 Å °-0.0506 Å °0.0132 Å °-0.0447 Å °0.0286 Å °-0.0305 Å °-0 Å °
Refinement TLS groupSelection details: all

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