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

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Basic information

Entry
Database: PDB / ID: 3ahz
TitleCrystal structure of beta-glucosidase from termite Neotermes koshunensis in complex with Tris
ComponentsBeta-glucosidase
KeywordsHYDROLASE / cellulases / glycosyl hydrolase / manganese enhancement
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
Biological speciesNeotermes koshunensis (cockroach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsJeng, W.-Y. / Liu, C.-I. / Wang, A.H.-J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural and functional analysis of three beta-glucosidases from bacterium Clostridium cellulovorans, fungus Trichoderma reesei and termite Neotermes koshunensis
Authors: Jeng, W.-Y. / Wang, N.-C. / Lin, M.-H. / Lin, C.-T. / Liaw, Y.-C. / Chang, W.-J. / Liu, C.-I. / Liang, P.-H. / Wang, A.H.-J.
History
DepositionMay 6, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8403
Polymers55,6261
Non-polymers2142
Water14,520806
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.959, 68.451, 75.228
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

21A-926-

HOH

31A-1122-

HOH

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Components

#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
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 42.56 %
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: 0.97315 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 16, 2008 / 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: 0.97315 Å / Relative weight: 1
ReflectionResolution: 1.34→30 Å / Num. all: 105275 / Num. obs: 105222 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.7
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.9 / Num. unique all: 10460 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBG

1cbg


Resolution: 1.34→25.6 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.289 / SU ML: 0.024 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14381 5061 5 %RANDOM
Rwork0.11526 ---
obs0.11671 95986 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å2-0.58 Å2
2---0.2 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.34→25.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 14 806 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223935
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.9365356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.885471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01224.279208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65115605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7111521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213115
X-RAY DIFFRACTIONr_mcbond_it1.4691.52348
X-RAY DIFFRACTIONr_mcangle_it2.11323776
X-RAY DIFFRACTIONr_scbond_it2.99631587
X-RAY DIFFRACTIONr_scangle_it4.2214.51580
X-RAY DIFFRACTIONr_rigid_bond_restr1.60733935
X-RAY DIFFRACTIONr_sphericity_free7.0243811
X-RAY DIFFRACTIONr_sphericity_bonded3.56933825
LS refinement shellResolution: 1.34→1.412 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.197 726 -
Rwork0.156 13134 -
obs--90.7 %
Refinement TLS params.Method: refined / Origin x: -29.1798 Å / Origin y: 87.7812 Å / Origin z: 15.7237 Å
111213212223313233
T0.0103 Å20.0024 Å2-0.0013 Å2-0.0067 Å2-0.0006 Å2--0.0099 Å2
L0.2408 °2-0.0285 °20.0471 °2-0.0857 °2-0.0574 °2--0.118 °2
S-0.0127 Å °-0.0373 Å °-0.0105 Å °0.0089 Å °0.0112 Å °-0.0152 Å °-0.015 Å °-0.0063 Å °0.0016 Å °

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