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- PDB-5wug: Expression, characterization and crystal structure of a novel bet... -

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Basic information

Entry
Database: PDB / ID: 5wug
TitleExpression, characterization and crystal structure of a novel beta-glucosidase from Paenibacillus barengoltzii
ComponentsBeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / GH family 3 / CBM6
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / 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, active site / Glycosyl hydrolases family 3 active site. / 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 ...Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.216 Å
AuthorsJiang, Z. / Wu, S. / Yang, D. / Qin, Z. / You, X. / Huang, P.
CitationJournal: J Food Sci Technol(China) / Year: 2019
Title: Expression, Biochemical Characterization and Structure Resolution of beta-glucosidase from Paenibacillus barengoltzii
Authors: Huang, P. / Wu, S. / Jiang, Z. / Yang, S.
History
DepositionDec 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase


Theoretical massNumber of molelcules
Total (without water)104,7641
Polymers104,7641
Non-polymers00
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.219, 75.786, 161.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucosidase /


Mass: 104763.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1P8VKA0, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 1.97 Å3/Da / Density % sol: 37.54 % / Description: long straight bar
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG 3350, 0.1M Bis-Tris pH 6.5, 0.2M Ammonium acetate
PH range: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 90-100
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CMOS / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.216→50 Å / Num. obs: 41633 / % possible obs: 99 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2474: ???)refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X40

2x40


Resolution: 2.216→42.724 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2036 2039 4.9 %
Rwork0.1573 --
obs0.1595 41630 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.216→42.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7146 0 0 657 7803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077285
X-RAY DIFFRACTIONf_angle_d0.8299892
X-RAY DIFFRACTIONf_dihedral_angle_d6.3184349
X-RAY DIFFRACTIONf_chiral_restr0.0511101
X-RAY DIFFRACTIONf_plane_restr0.0051305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2156-2.26710.2641340.17592427X-RAY DIFFRACTION94
2.2671-2.32380.23351410.17322615X-RAY DIFFRACTION100
2.3238-2.38670.25861200.17372627X-RAY DIFFRACTION100
2.3867-2.45690.25011350.17532619X-RAY DIFFRACTION100
2.4569-2.53620.22661370.17942640X-RAY DIFFRACTION100
2.5362-2.62680.23211350.17632623X-RAY DIFFRACTION100
2.6268-2.7320.22991260.17182646X-RAY DIFFRACTION100
2.732-2.85630.25111410.17982600X-RAY DIFFRACTION100
2.8563-3.00680.24231450.17582641X-RAY DIFFRACTION100
3.0068-3.19520.2011430.17372654X-RAY DIFFRACTION100
3.1952-3.44180.22551260.16742660X-RAY DIFFRACTION100
3.4418-3.78790.20481350.14552664X-RAY DIFFRACTION100
3.7879-4.33560.14771400.12932654X-RAY DIFFRACTION99
4.3356-5.46060.15911410.12792720X-RAY DIFFRACTION100
5.4606-42.73150.16941400.15112804X-RAY DIFFRACTION98

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