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

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Basic information

Entry
Database: PDB / ID: 3vip
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-GOI / 5H-dibenzo[b,f]azepine / Beta-glucosidase
Similarity search - Component
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)56,5167
Polymers55,6111
Non-polymers9056
Water11,530640
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)113,03314
Polymers111,2232
Non-polymers1,81012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2680 Å2
ΔGint-28 kcal/mol
Surface area32580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.785, 68.500, 75.075
Angle α, β, γ (deg.)90.00, 95.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-511-

CL

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Components

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Protein , 1 types, 1 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

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Non-polymers , 6 types, 646 molecules

#2: Chemical ChemComp-GOI / 2-{4-[3-(5H-dibenzo[b,f]azepin-5-yl)propyl]piperazin-1-yl}ethyl beta-D-glucopyranoside


Mass: 525.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H39N3O6
#3: Chemical ChemComp-ONB / 5H-dibenzo[b,f]azepine


Mass: 193.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 640 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2011 / 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: 1.28→30 Å / Num. all: 120278 / Num. obs: 119961 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 39.3
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 8.3 / Num. unique all: 11983 / % possible all: 99.8

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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: 1.28→22.9 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.947 / SU ML: 0.019 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14383 6025 5 %RANDOM
Rwork0.12045 ---
obs0.12162 119863 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å2-0.44 Å2
2---0.03 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 62 640 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9535597
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09524.279215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69515637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.051523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213253
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_it1.2461.52395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8823876
X-RAY DIFFRACTIONr_scbond_it2.7431697
X-RAY DIFFRACTIONr_scangle_it3.9944.51704
X-RAY DIFFRACTIONr_rigid_bond_restr1.2434092
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.279→1.348 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.174 858 -
Rwork0.136 16313 -
obs-17171 98.44 %
Refinement TLS params.Method: refined / Origin x: -29.1475 Å / Origin y: 87.8346 Å / Origin z: 15.5466 Å
111213212223313233
T0.0141 Å20.002 Å2-0.0022 Å2-0.0063 Å2-0.0003 Å2--0.0152 Å2
L0.2742 °2-0.0271 °20.0527 °2-0.0925 °2-0.0599 °2--0.1318 °2
S-0.0102 Å °-0.0391 Å °-0.012 Å °0.0053 Å °0.0107 Å °-0.0123 Å °-0.0121 Å °-0.0083 Å °-0.0006 Å °

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