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- PDB-1e4i: 2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of t... -

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Basic information

Entry
Database: PDB / ID: 1e4i
Title2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / FAMILY 1 GLYCOSYL HYDROLASE / COVALENT ENZYME-GLYCOSIDE INTERMEDIATE / ALPHA/BETA BARREL
Function / homology
Function and homology information


scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / 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 / Chem-NFG / Beta-glucosidase A
Similarity search - Component
Biological speciesBACILLUS POLYMYXA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSanz-Aparicio, J. / Gonzalez, B. / Hermoso, J.A. / Arribas, J.C. / Canada, F.J. / Polaina, J.
Citation
Journal: Proteins: Struct.,Funct., Genet. / Year: 1998
Title: Structural Basis of Increased Resistance to Thermal Denaturation Induced by Single Amino Acid Substitution in the Sequence of Beta-Glucosidase a from Bacillus Polymyxa.
Authors: Sanz-Aparicio, J. / Hermoso, J.A. / Martinez-Ripoll, M. / Gonzalez, B. / Lopez-Camacho, C. / Polaina, J.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal Structure of Beta-Glucosidase a from Bacillus Polymyxa: Insights Into the Catalytic Activity in Family 1 Glycosyl Hydrolases
Authors: Sanz-Aparicio, J. / Hermoso, J.A. / Martinez-Ripoll, M. / Gonzalez, B. / Lopez-Camacho, C. / Polaina, J.
History
DepositionJul 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references / Structure summary / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jul 1, 2020Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.4Jul 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 1.5Dec 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

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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)52,0973
Polymers51,5671
Non-polymers5302
Water4,216234
1
A: BETA-GLUCOSIDASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)416,77624
Polymers412,5338
Non-polymers4,24316
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area20070 Å2
ΔGint-37.4 kcal/mol
Surface area140580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.230, 136.230, 173.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
DetailsBIOMOLECULE

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Components

#1: Protein BETA-GLUCOSIDASE /


Mass: 51566.570 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS POLYMYXA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P22073, 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: Sugar ChemComp-NFG / 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-D-glucoside / 2,4-dinitrophenyl 2-deoxy-2-fluoro-glucoside


Type: D-saccharide / Mass: 348.238 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13FN2O9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growpH: 7
Details: DROP: 10 MICROL PROTEIN (8 MG/ML)+ 5 MICROL PP(1M, PH=7)+5 MICROL INH (5MM) RESERVOIR: 1.3M PP, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.989
DetectorDetector: CCD / Date: Oct 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.96→42.3 Å / Num. obs: 56246 / % possible obs: 98 % / Redundancy: 5 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 2→2.1 Å / Rsym value: 0.34 / % possible all: 95

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BGA

1bga


Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -7 %RANDOM
Rwork0.21 ---
obs0.21 53692 98 %-
Displacement parametersBiso mean: 15.9 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 35 234 3913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.93
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.28 -
Rwork0.26 5860
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH3.CHO
X-RAY DIFFRACTION3PARAM3.CHO

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