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- PDB-3vin: Crystal structure of beta-glucosidase from termite Neotermes kosh... -

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Basic information

Entry
Database: PDB / ID: 3vin
TitleCrystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with a new glucopyranosidic product
ComponentsBeta-glucosidase
KeywordsHYDROLASE / CELLULASES / GLYCOSYL HYDROLASE
Function / homology
Function and homology information


beta-glucosidase / beta-glucosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-GBH / Beta-glucosidase
Similarity search - Component
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsJeng, W.Y. / Liu, C.I. / Wang, A.H.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: High-resolution structures of Neotermes koshunensis beta-glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates
Authors: Jeng, W.Y. / Wang, N.C. / Lin, C.T. / Chang, W.J. / Liu, C.I. / Wang, A.H.J.
History
DepositionOct 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_ref_seq_dif ...chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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)56,1986
Polymers55,6111
Non-polymers5865
Water12,196677
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-glucosidase
hetero molecules

A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,39612
Polymers111,2232
Non-polymers1,17310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2680 Å2
ΔGint-28 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.152, 68.573, 75.638
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-510-

CL

21A-511-

CL

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-glucosidase


Mass: 55611.492 Da / Num. of mol.: 1 / Mutation: E193D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neotermes koshunensis (cockroach) / Gene: NkBG / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: Q8T0W7, beta-glucosidase
#2: Sugar ChemComp-GBH / 2-{4-[2-(beta-D-glucopyranosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid / 2-{4-[2-(beta-D-glucosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid / 2-{4-[2-(D-glucosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid / 2-{4-[2-(glucosyloxy)ethyl]piperazin-1-yl}ethanesulfonic acid


Type: D-saccharide / Mass: 400.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28N2O9S

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Non-polymers , 4 types, 681 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 18-21%(w/v) PEG 3350, 0.1-0.25M MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 6, 2010
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.13→22.5 Å / Num. all: 176832 / Num. obs: 173272 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.7
Reflection shellResolution: 1.13→1.17 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.4 / Num. unique all: 17555 / % possible all: 96.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AHZ

3ahz


Resolution: 1.13→22.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.945 / SU ML: 0.02 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15626 8684 5 %RANDOM
Rwork0.13508 ---
obs0.13617 173141 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.103 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.42 Å2
2---0.42 Å20 Å2
3---1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.13→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 35 677 4522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.9445537
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9235501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33124.398216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09115634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6031522
X-RAY DIFFRACTIONr_chiral_restr0.0970.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2951.52389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84623863
X-RAY DIFFRACTIONr_scbond_it2.68431661
X-RAY DIFFRACTIONr_scangle_it3.8164.51659
X-RAY DIFFRACTIONr_rigid_bond_restr1.27934050
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.129→1.19 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.256 1160 -
Rwork0.232 23417 -
obs-24577 95.55 %
Refinement TLS params.Method: refined / Origin x: -29.2359 Å / Origin y: 87.8605 Å / Origin z: 15.5737 Å
111213212223313233
T0.0165 Å20.002 Å20.0012 Å2-0.0132 Å20.0016 Å2--0.0049 Å2
L0.3334 °2-0.0314 °20.0519 °2-0.1822 °2-0.0545 °2--0.1645 °2
S-0.012 Å °-0.0512 Å °-0.0184 Å °0.0272 Å °0.0107 Å °-0.0207 Å °-0.0145 Å °0.0023 Å °0.0013 Å °

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