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- PDB-1np2: Crystal structure of thermostable beta-glycosidase from thermophi... -

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Basic information

Entry
Database: PDB / ID: 1np2
TitleCrystal structure of thermostable beta-glycosidase from thermophilic eubacterium Thermus nonproteolyticus HG102
Componentsbeta-glycosidase
KeywordsHYDROLASE / TIM barrel
Function / homology
Function and homology information


: / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase, family 1, beta-glucosidase / Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus nonproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiang, D.C. / Chang, W.R. / Wang, X.Q. / He, X.Y.
Citation
Journal: J.Bacteriol. / Year: 2003
Title: Structural Basis for Thermostability of beta-Glycosidase from the Thermophilic Eubacterium Thermus nonproteolyticus HG102.
Authors: Wang, X. / He, X. / Yang, S. / An, X. / Chang, W. / Liang, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Overexpression, purification, crystallization and preliminary crystallographic studies on a thermostable beta-glycosidase from Thermus nonproteolyticus HG102.
Authors: He, X.Y. / Wang, X.Q. / Yang, S.J. / Chang, W.R. / Liang, D.C.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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-glycosidase
B: beta-glycosidase


Theoretical massNumber of molelcules
Total (without water)98,1122
Polymers98,1122
Non-polymers00
Water6,017334
1
A: beta-glycosidase


Theoretical massNumber of molelcules
Total (without water)49,0561
Polymers49,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-glycosidase


Theoretical massNumber of molelcules
Total (without water)49,0561
Polymers49,0561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.700, 94.755, 176.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer enzyme

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Components

#1: Protein beta-glycosidase


Mass: 49056.168 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus nonproteolyticus (bacteria) / Strain: HG102 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9L794, beta-glucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.79 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: He, X.Y., (2001) Acta Crystallogr.,Sect.D, 57, 1650.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlprotein1drop
25 mMHEPES1droppH7.5
320 %MPD1reservoir
40.2 M1reservoirNaCl
50.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→83.51 Å / Num. all: 44647 / Num. obs: 42023 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.182 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.2 / % possible all: 73.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 41963 / % possible obs: 94 %
Reflection shell
*PLUS
% possible obs: 73.4 % / Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1BGA

1bga


Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2102 -random
Rwork0.23 ---
obs0.23 41963 94 %-
all-44647 --
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6822 0 0 334 7156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.38
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.98
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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