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

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Basic information

Entry
Database: PDB / ID: 3vig
TitleCrystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with 1-deoxynojirimycin
ComponentsBeta-glucosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CELLULASES / GLYCOSYL HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
1-DEOXYNOJIRIMYCIN / Beta-glucosidase
Similarity search - Component
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 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)56,1786
Polymers55,6261
Non-polymers5525
Water12,232679
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)112,35512
Polymers111,2512
Non-polymers1,10410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area4530 Å2
ΔGint-9 kcal/mol
Surface area32010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.108, 68.559, 75.144
Angle α, β, γ (deg.)90.00, 95.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-511-

CL

21A-669-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-glucosidase


Mass: 55625.516 Da / Num. of mol.: 1
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, 684 molecules

#2: Chemical ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2009 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.99→30 Å / Num. all: 260641 / Num. obs: 259744 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 31.7
Reflection shellResolution: 0.99→1.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2 / Num. unique all: 25975 / % possible all: 99.5

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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: 0.99→28.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.586 / SU ML: 0.014 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14648 13058 5 %RANDOM
Rwork0.13013 ---
obs0.13097 259516 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-0.53 Å2
2---0.24 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 0.99→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 34 679 4524
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_deg1.4071.9445535
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28524.252214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.68915636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0461523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2574
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213201
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_it1.2191.52389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79823864
X-RAY DIFFRACTIONr_scbond_it2.48531661
X-RAY DIFFRACTIONr_scangle_it3.6124.51656
X-RAY DIFFRACTIONr_rigid_bond_restr1.18634050
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.989→1.043 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.254 1837 -
Rwork0.252 35710 -
obs-37547 98.94 %
Refinement TLS params.Method: refined / Origin x: -29.2624 Å / Origin y: 87.7384 Å / Origin z: 15.6168 Å
111213212223313233
T0.0081 Å20.0028 Å20.0019 Å2-0.0075 Å2-0.0012 Å2--0.0053 Å2
L0.1795 °2-0.0193 °20.0315 °2-0.0714 °2-0.0465 °2--0.0798 °2
S-0.0138 Å °-0.0281 Å °-0.0071 Å °0.0085 Å °0.0118 Å °-0.0146 Å °-0.0129 Å °-0.0073 Å °0.0019 Å °

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