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

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Basic information

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


: / beta-glucosidase / beta-glucosidase activity / 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 ...: / 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
beta-D-mannopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesPaenibacillus barengoltzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsJiang, Z. / Wu, S. / Yang, D. / Qin, Z. / You, X. / Huang, P.
CitationJournal: To Be Published
Title: Expression, characterization and crystal structure of a novel beta-glucosidase from Paenibacillus barengoltzii
Authors: Jiang, Z. / Wu, S. / Yang, D. / Qin, Z. / You, X. / Huang, P.
History
DepositionDec 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 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: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9442
Polymers104,7641
Non-polymers1801
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint2 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.695, 75.215, 160.816
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: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.93 Å3/Da / Density % sol: 36.11 %
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: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.294→50 Å / Num. obs: 35790 / % possible obs: 97 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 25.917
Reflection shellResolution: 2.294→2.33 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
PHENIX(dev_2474: ???)refinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WUG

5wug


Resolution: 2.294→49.902 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1760 4.92 %
Rwork0.17 --
obs0.1729 35773 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.294→49.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7079 0 12 247 7338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097224
X-RAY DIFFRACTIONf_angle_d0.9759807
X-RAY DIFFRACTIONf_dihedral_angle_d6.5314312
X-RAY DIFFRACTIONf_chiral_restr0.0581098
X-RAY DIFFRACTIONf_plane_restr0.0061292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.294-2.3560.317860.20891953X-RAY DIFFRACTION73
2.356-2.42530.26771190.19662330X-RAY DIFFRACTION87
2.4253-2.50360.23491390.20152560X-RAY DIFFRACTION96
2.5036-2.59310.29671490.18952646X-RAY DIFFRACTION99
2.5931-2.69690.26051370.19522667X-RAY DIFFRACTION100
2.6969-2.81960.26711360.1872675X-RAY DIFFRACTION100
2.8196-2.96830.25871270.18392688X-RAY DIFFRACTION100
2.9683-3.15420.27671510.18872688X-RAY DIFFRACTION100
3.1542-3.39770.25591460.17692677X-RAY DIFFRACTION100
3.3977-3.73950.21341630.15462720X-RAY DIFFRACTION100
3.7395-4.28040.22211320.14212721X-RAY DIFFRACTION100
4.2804-5.39180.17941240.14022794X-RAY DIFFRACTION100
5.3918-49.91380.19131510.17532896X-RAY DIFFRACTION100

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