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- PDB-2o9t: beta-glucosidase B from Bacillus polymyxa complexed with glucose -

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Basic information

Entry
Database: PDB / ID: 2o9t
Titlebeta-glucosidase B from Bacillus polymyxa complexed with glucose
ComponentsBeta-glucosidase B
KeywordsHYDROLASE / beta-glucosidase / glycosyl hydrolase family 1 / glucose complex
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-glucosidase B
Similarity search - Component
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsIsorna, P. / Polaina, J. / Sanz-Aparicio, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Paenibacillus polymyxa beta-Glucosidase B Complexes Reveal the Molecular Basis of Substrate Specificity and Give New Insights into the Catalytic Machinery of Family I Glycosidases
Authors: Isorna, P. / Polaina, J. / Latorre-Garcia, L. / Canada, F.J. / Gonzalez, B. / Sanz-Aparicio, J.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7282
Polymers52,5481
Non-polymers1801
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.330, 75.580, 88.950
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 B / Gentiobiase / Cellobiase / Beta-D- glucoside glucohydrolase / Amygdalase


Mass: 52547.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Plasmid: DpuC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P22505, beta-glucosidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growMethod: vapor diffusion / pH: 6.5
Details: 30% PEG550MME, 0.05M Cl2Ca, 0.1M bis/tris, pH 6.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jul 1, 2005 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 26625 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Χ2: 1.963 / Net I/σ(I): 25.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.232.40.28825621.70297.4
2.23-2.322.50.22426191.56999.6
2.32-2.422.70.18826241.72799.5
2.42-2.552.80.1426451.71899.9
2.55-2.7130.10926441.73100
2.71-2.923.20.07926681.749100
2.92-3.213.50.05426611.652100
3.21-3.683.80.03726881.69499.7
3.68-4.634.60.03526952.22499.1
4.63-5050.03828192.73698.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2O9P

2o9p


Resolution: 2.15→18.33 Å / FOM work R set: 0.785 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1722 6.4 %random
Rwork0.245 ---
obs-25353 94.6 %-
Solvent computationBsol: 73.956 Å2
Displacement parametersBiso mean: 35.879 Å2
Baniso -1Baniso -2Baniso -3
1-5.074 Å20 Å20 Å2
2---15.85 Å20 Å2
3---10.776 Å2
Refinement stepCycle: LAST / Resolution: 2.15→18.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 12 127 3764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.313
X-RAY DIFFRACTIONc_mcbond_it1.2491.5
X-RAY DIFFRACTIONc_scbond_it1.9082
X-RAY DIFFRACTIONc_mcangle_it1.8582
X-RAY DIFFRACTIONc_scangle_it2.6912.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 34

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.15-2.170.419350.395584619
2.17-2.190.37460.378609655
2.19-2.220.456530.374646699
2.22-2.240.378570.348638695
2.24-2.270.342480.304640688
2.27-2.290.327450.297655700
2.29-2.320.349500.269653703
2.32-2.350.287480.29668716
2.35-2.380.303410.277682723
2.38-2.410.37470.271678725
2.41-2.450.38480.274675723
2.45-2.490.307480.26701749
2.49-2.520.34460.266674720
2.52-2.570.314490.288689738
2.57-2.610.294600.232695755
2.61-2.660.238500.242707757
2.66-2.710.334500.251694744
2.71-2.760.361660.254680746
2.76-2.820.262380.275731769
2.82-2.890.327520.249703755
2.89-2.960.345550.261715770
2.96-3.040.386510.277719770
3.04-3.130.262490.269715764
3.13-3.230.274550.242725780
3.23-3.350.305470.247739786
3.35-3.480.233420.231739781
3.48-3.640.305540.23733787
3.64-3.830.224630.212716779
3.83-4.070.257580.216723781
4.07-4.390.208510.184750801
4.39-4.830.195550.188715770
4.83-5.530.224640.207749813
5.53-6.970.245600.241755815
6.97-500.274410.288736777
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5glu.paramglu.top

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