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- PDB-2x42: Structure of beta-glucosidase 3B from Thermotoga neapolitana in c... -

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Basic information

Entry
Database: PDB / ID: 2x42
TitleStructure of beta-glucosidase 3B from Thermotoga neapolitana in complex with alpha-D-glucose
ComponentsBETA-GLUCOSIDASE
KeywordsHYDROLASE / TIM BARREL FOLD / FIBRONECTIN TYPE III FOLD
Function / homology
Function and homology information


scopolin beta-glucosidase activity / glucan catabolic process / beta-glucosidase / beta-glucosidase activity
Similarity search - Function
Glycoside hydrolase family 3 C-terminal domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily ...Glycoside hydrolase family 3 C-terminal domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Fibronectin type III-like domain / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase family 3 C-terminal domain / Glycosyl hydrolase family 3 C-terminal domain / Glycoside hydrolase family 3 C-terminal domain superfamily / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / alpha-D-glucopyranose / Beta-glucosidase
Similarity search - Component
Biological speciesTHERMOTOGA NEAPOLITANA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsPozzo, T. / Karlsson, E.N. / Logan, D.T.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Structural and Functional Analysis of Beta-Glucosidase 3B from Thermotoga Neapolitana: A Thermostable 3-Domain Representative of Glycoside Hydrolase Family 3
Authors: Pozzo, T. / Linares Pasten, J. / Karlsson, E.N. / Logan, D.T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of Thermotoga Neapolitana Beta-Glucosidase B.
Authors: Turner, P. / Pramhed, A. / Kanders, E. / Hedstrom, M. / Karlsson, E.N. / Logan, D.T.
History
DepositionJan 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)81,7186
Polymers81,2181
Non-polymers5005
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.550, 128.160, 175.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BETA-GLUCOSIDASE / BETA-GLUCOSIDASE 3B


Mass: 81217.852 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA NEAPOLITANA (bacteria) / Strain: DSM 4359 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER(DE3) / References: UniProt: Q0GC07, beta-glucosidase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 242 TO ALA

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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: 2.57 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.4
Details: 3-5 MG/ML PROTEIN, 16-18 % (V/V) PEG 3350, 0.2 M NABR, 90 MM BIS-TRIS PROPANE PH 7.4, 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Sep 24, 2008 / Details: MULTILAYER MIRRORS
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.1→29.2 Å / Num. obs: 47706 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 32.69 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / % possible all: 78.3

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
REFMACphasing
PHENIXphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X40

2x40


Resolution: 2.099→29.275 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 2402 5 %
Rwork0.1715 --
obs0.1737 47687 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.433 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.099→29.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 16 442 6134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055807
X-RAY DIFFRACTIONf_angle_d0.8837853
X-RAY DIFFRACTIONf_dihedral_angle_d15.7932171
X-RAY DIFFRACTIONf_chiral_restr0.063851
X-RAY DIFFRACTIONf_plane_restr0.0031026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0991-2.14190.32441170.27141991X-RAY DIFFRACTION73
2.1419-2.18850.24961430.23092612X-RAY DIFFRACTION95
2.1885-2.23930.23611230.20762634X-RAY DIFFRACTION96
2.2393-2.29530.26851320.2082643X-RAY DIFFRACTION97
2.2953-2.35740.28421450.20672602X-RAY DIFFRACTION96
2.3574-2.42670.27491420.2022664X-RAY DIFFRACTION97
2.4267-2.5050.29041420.1952679X-RAY DIFFRACTION98
2.505-2.59450.25141440.18922685X-RAY DIFFRACTION98
2.5945-2.69830.24321350.18732694X-RAY DIFFRACTION98
2.6983-2.8210.22291470.17642695X-RAY DIFFRACTION99
2.821-2.96960.24231520.17692731X-RAY DIFFRACTION98
2.9696-3.15540.22321360.18032721X-RAY DIFFRACTION99
3.1554-3.39870.20791450.16352753X-RAY DIFFRACTION99
3.3987-3.74010.18871320.1472757X-RAY DIFFRACTION99
3.7401-4.27990.15451460.13092774X-RAY DIFFRACTION99
4.2799-5.38670.18491480.13172799X-RAY DIFFRACTION99
5.3867-29.27780.17571730.16292851X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.61450.3181-0.06860.68530.00520.8042-0.02480.01940.0431-0.14510.0334-0.0371-0.20.1215-0.01310.2369-0.04360.00280.2111-0.01140.1675-6.16124.8398-21.9921
20.4775-0.13320.3961.22280.14151.5861-0.0506-0.0460.0486-0.1640.03540.3947-0.1135-0.35210.02360.20150.0075-0.10870.30640.00920.2949-39.287912.8605-25.4965
30.0611-0.0771-0.02580.3548-0.08810.3906-0.0012-0.0893-0.01410.03770.02560.10870.0292-0.129-0.02040.18870.0024-0.00940.23480.00240.1945-22.02435.8523-8.6622
40.4544-0.43070.0930.9695-0.58630.50580.0473-0.0108-0.1644-0.161-0.0172-0.05350.26170.1766-0.0250.23890.01620.00550.2531-0.02960.1838-10.026-8.2781-20.389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:320)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 321:536)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 537:599)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 600:721)

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