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- PDB-2o9p: beta-glucosidase B from Paenibacillus polymyxa -

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Basic information

Entry
Database: PDB / ID: 2o9p
Titlebeta-glucosidase B from Paenibacillus polymyxa
ComponentsBeta-glucosidase B
KeywordsHYDROLASE / beta-glucosidase / family 1 glycoside hydrolase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process
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
Biological speciesPaenibacillus polymyxa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Beta-glucosidase B


Theoretical massNumber of molelcules
Total (without water)52,5481
Polymers52,5481
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.895, 74.958, 88.660
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) / Gene: bglB / Plasmid: DpUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1BLUE / References: UniProt: P22505, beta-glucosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growMethod: vapor diffusion / pH: 6.5
Details: 30% PEG 550 MME, 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: OTHER / Wavelength: 1.5418 Å
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→50 Å / Num. obs: 32444 / % possible obs: 99.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Χ2: 1.997 / Net I/σ(I): 17.2
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.48 / Num. unique all: 3034 / Χ2: 1.616 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E4I

1e4i


Resolution: 2.1→50 Å / FOM work R set: 0.788 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1944 6.9 %RANDOM
Rwork0.235 ---
obs-28217 99.9 %-
Solvent computationBsol: 56.301 Å2
Displacement parametersBiso mean: 36.014 Å2
Baniso -1Baniso -2Baniso -3
1-4.267 Å20 Å20 Å2
2---12.015 Å20 Å2
3---7.748 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 0 138 3764
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_scbond_it2.0052
X-RAY DIFFRACTIONc_mcangle_it2.0172
X-RAY DIFFRACTIONc_scangle_it2.8562.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 38

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.120.44580.41668726
2.12-2.140.377420.361698740
2.14-2.160.335550.336674729
2.16-2.180.327530.332645698
2.18-2.20.356410.32714755
2.2-2.220.384470.296679726
2.22-2.250.349500.278664714
2.25-2.270.336580.279691749
2.27-2.30.345430.271673716
2.3-2.330.385370.283699736
2.33-2.350.355490.286708757
2.35-2.380.285440.266662706
2.38-2.410.273570.227694751
2.41-2.450.34530.249676729
2.45-2.480.321410.237676717
2.48-2.520.28510.248712763
2.52-2.560.313490.245658707
2.56-2.60.291530.234692745
2.6-2.650.252570.223680737
2.65-2.690.314600.231671731
2.69-2.750.349520.243684736
2.75-2.80.247580.231681739
2.8-2.860.333500.234707757
2.86-2.930.302490.246665714
2.93-30.319550.245693748
3-3.080.321470.23703750
3.08-3.170.343560.252680736
3.17-3.280.29580.242688746
3.28-3.390.209550.22693748
3.39-3.530.205450.209701746
3.53-3.690.314480.223711759
3.69-3.890.259560.2689745
3.89-4.130.266530.207704757
4.13-4.450.217540.175704758
4.45-4.90.219480.19715763
4.9-5.60.231560.216708764
5.6-7.060.22540.259730784
7.06-500.010.265520.269783835
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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