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- PDB-1ug6: Structure of beta-glucosidase at atomic resolution from thermus t... -

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Basic information

Entry
Database: PDB / ID: 1ug6
TitleStructure of beta-glucosidase at atomic resolution from thermus thermophilus HB8
Componentsbeta-glycosidase
KeywordsHYDROLASE / GLUCOSIDASE / ATOMIC RESOLUTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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 thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsLokanath, N.K. / Shiromizu, I. / Miyano, M. / Yokoyama, S. / Kuramitsu, S. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Beta-Glucosidase at Atomic Resolution from Thermus Thermophilus Hb8
Authors: Lokanath, N.K. / Shiromizu, I. / Miyano, M. / Yokoyama, S. / Kuramitsu, S. / Kunishima, N.
History
DepositionJun 12, 2003Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 24, 2003ID: 1UAH
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0645
Polymers48,6961
Non-polymers3684
Water9,566531
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.092, 116.463, 87.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1434-

HOH

DetailsOnly one molecule in the asymmetric unit and also in solution, which was confirmed by DLS experiment

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Components

#1: Protein beta-glycosidase / beta-Glucosidase protein


Mass: 48695.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q8GEB3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.5 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4
Details: PEG 4000, HEPES, Calcium chloride, pH 7.40, MICROBATCH, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 9, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.99→40 Å / Num. all: 306077 / Num. obs: 305837 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 5.68 Å2 / Rmerge(I) obs: 0.048
Reflection shellResolution: 0.99→1.03 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.27refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4I

1e4i


Resolution: 0.99→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.13 15443 5 %RANDOM
Rwork0.121 ---
all0.122 306077 --
obs0.122 305837 99.9 %-
Refinement stepCycle: LAST / Resolution: 0.99→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 24 531 3968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.007
X-RAY DIFFRACTIONr_angle_refined_deg1.2

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