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

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Basic information

Entry
Database: PDB / ID: 3vil
TitleCrystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with salicin
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
2-(hydroxymethyl)phenyl beta-D-glucopyranoside / 2-(hydroxymethyl)phenol / Beta-glucosidase
Similarity search - Component
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1507
Polymers55,5831
Non-polymers5666
Water12,052669
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)112,30014
Polymers111,1672
Non-polymers1,13312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2430 Å2
ΔGint-27 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.908, 68.536, 75.663
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-511-

CL

21A-512-

CL

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Beta-glucosidase


Mass: 55583.480 Da / Num. of mol.: 1 / Mutation: E193S
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-SA0 / 2-(hydroxymethyl)phenyl beta-D-glucopyranoside / Salicin / 2-(hydroxymethyl)phenyl beta-D-glucoside / 2-(hydroxymethyl)phenyl D-glucoside / 2-(hydroxymethyl)phenyl glucoside


Type: D-saccharide / Mass: 286.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H18O7

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Non-polymers , 5 types, 674 molecules

#3: Chemical ChemComp-SA9 / 2-(hydroxymethyl)phenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 669 / 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: 42.96 %
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: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2010 / Details: Vertically Focusing Mirror
RadiationMonochromator: Horizontally Focusing Single Crystal Si(111) Bent Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. all: 167114 / Num. obs: 166145 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 34.5
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.7 / Num. unique all: 16643 / % possible all: 99.7

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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: 1.15→25.2 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.971 / SU ML: 0.02 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15428 8352 5 %RANDOM
Rwork0.12807 ---
obs0.12937 165967 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-0.46 Å2
2---0.17 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.15→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3808 0 36 669 4513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9435523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.945499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84124.252214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.66115632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2711523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213213
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_it1.3791.52386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98523856
X-RAY DIFFRACTIONr_scbond_it2.96331657
X-RAY DIFFRACTIONr_scangle_it4.214.51653
X-RAY DIFFRACTIONr_rigid_bond_restr1.42234043
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.15→1.212 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.235 1242 -
Rwork0.216 22871 -
obs-24113 99.31 %
Refinement TLS params.Method: refined / Origin x: -29.3385 Å / Origin y: 87.8597 Å / Origin z: 15.7032 Å
111213212223313233
T0.0173 Å20.0039 Å2-0.0006 Å2-0.0132 Å20.0006 Å2--0.0124 Å2
L0.4338 °2-0.0183 °20.0774 °2-0.189 °2-0.0583 °2--0.1967 °2
S-0.0117 Å °-0.0703 Å °-0.0186 Å °0.0302 Å °0.0145 Å °-0.0266 Å °-0.0125 Å °-0.0024 Å °-0.0028 Å °

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