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- PDB-2jie: BETA-GLUCOSIDASE B FROM BACILLUS POLYMYXA COMPLEXED WITH 2-F-GLUCOSE -

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Basic information

Entry
Database: PDB / ID: 2jie
TitleBETA-GLUCOSIDASE B FROM BACILLUS POLYMYXA COMPLEXED WITH 2-F-GLUCOSE
ComponentsBETA-GLUCOSIDASE B
KeywordsHYDROLASE / GLYCOSYL HYDROLASE FAMILY 1 / CARBOHYDRATE METABOLISM / POLYSACCHARIDE DEGRADATION / 2-F-GLUCOSE COMPLEX / CELLULOSE DEGRADATION / GLYCOSIDASE / BETA-GLUCOSIDASE
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
2-deoxy-2-fluoro-alpha-D-glucopyranose / Beta-glucosidase B
Similarity search - Component
Biological speciesPAENIBACILLUS POLYMYXA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionFeb 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_database_status / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)52,6402
Polymers52,4581
Non-polymers1821
Water2,324129
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.236, 74.647, 88.754
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: 52457.844 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-448
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-G2F / 2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-alpha-D-glucose / 2-deoxy-2-fluoro-D-glucose / 2-deoxy-2-fluoro-glucose


Type: D-saccharide, alpha linking / Mass: 182.147 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11FO5
IdentifierTypeProgram
a-D-Glcp2fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHIS TAG

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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: 2.6 Å3/Da / Density % sol: 40 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 24641 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4I

1e4i


Resolution: 2.3→25 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.3061 1477 6.8 %RANDOM
Rwork0.2498 ---
obs0.2498 21471 99.3 %-
Solvent computationSolvent model: RESTRAINED / Bsol: 51.5349 Å2 / ksol: 0.38643 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.72 Å20 Å20 Å2
2---26.277 Å20 Å2
3---8.556 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 11 129 3759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009564
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.63811
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.33 Å / Total num. of bins used: 29 /
RfactorNum. reflection
Rfree0.41 52
Rwork0.39 671
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3_MOD.CHO

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