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- PDB-2x40: Structure of beta-glucosidase 3B from Thermotoga neapolitana in c... -

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Basic information

Entry
Database: PDB / ID: 2x40
TitleStructure of beta-glucosidase 3B from Thermotoga neapolitana in complex with glycerol
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 / Beta-glucosidase
Similarity search - Component
Biological speciesTHERMOTOGA NEAPOLITANA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.313 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 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)81,6746
Polymers81,2621
Non-polymers4125
Water4,161231
1
A: BETA-GLUCOSIDASE
hetero molecules

A: BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,34712
Polymers162,5242
Non-polymers82310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4290 Å2
ΔGint-5.8 kcal/mol
Surface area50070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.946, 127.246, 175.209
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: 81261.867 Da / Num. of mol.: 1
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: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#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.: 231 / 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: 2.57 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.4
Details: PROTEIN 3-5 MG/ML, 16% PEG 3350, 0.1 M KBR, 90 MM BIS-TRIS PROPANE PH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 21, 2006 / Details: MULTILAYER MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→34.5 Å / Num. obs: 37161 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 43.22 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.313→34.453 Å / SU ML: 0.32 / σ(F): 1.37 / Phase error: 25.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1858 5 %
Rwork0.1737 --
obs0.1766 36846 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.019 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 55.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.5703 Å20 Å2-0 Å2
2--12.3859 Å20 Å2
3----6.8156 Å2
Refinement stepCycle: LAST / Resolution: 2.313→34.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 10 231 5901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055784
X-RAY DIFFRACTIONf_angle_d0.8627820
X-RAY DIFFRACTIONf_dihedral_angle_d16.242159
X-RAY DIFFRACTIONf_chiral_restr0.062843
X-RAY DIFFRACTIONf_plane_restr0.0031024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3129-2.37540.39821240.3682605X-RAY DIFFRACTION97
2.3754-2.44530.38311430.3052637X-RAY DIFFRACTION100
2.4453-2.52420.31421470.25272662X-RAY DIFFRACTION100
2.5242-2.61440.27761450.22182671X-RAY DIFFRACTION100
2.6144-2.7190.31391190.21062707X-RAY DIFFRACTION100
2.719-2.84270.28951650.20022661X-RAY DIFFRACTION100
2.8427-2.99250.2581520.18592658X-RAY DIFFRACTION100
2.9925-3.17990.26061420.18122700X-RAY DIFFRACTION100
3.1799-3.42520.23271500.15912678X-RAY DIFFRACTION100
3.4252-3.76950.21011540.14882699X-RAY DIFFRACTION100
3.7695-4.3140.1921490.12842718X-RAY DIFFRACTION100
4.314-5.43180.19211380.13012749X-RAY DIFFRACTION100
5.4318-34.45710.18631300.1652843X-RAY DIFFRACTION99
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)
10.69360.4687-0.32020.9597-0.18580.62870.0074-0.0090.0505-0.1554-0.0061-0.0438-0.40160.3061-0.00220.443-0.1576-0.02790.32910.02420.2251-6.236724.9929-21.9898
20.6706-0.48930.85781.29290.23362.1202-0.1181-0.0602-0.0154-0.2440.0760.3737-0.2107-0.47840.02380.2669-0.0066-0.15290.36620.0510.3005-39.518912.6983-25.3878
30.5207-0.272-0.04280.7505-0.54430.5181-0.0023-0.1594-0.075-0.01710.05940.1468-0.0799-0.0891-0.06410.2559-0.0186-0.01970.28270.02750.2497-22.00625.8584-8.6193
40.6535-0.8659-0.0351.7715-0.85751.4359-0.02940.013-0.248-0.44530.0215-0.0040.51390.550.04130.39820.04340.05540.38-0.00350.2625-9.9411-8.1932-20.4844
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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