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- PDB-8wfu: Crystal structure of beta-glucosidase from Thermoanaerobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8wfu
TitleCrystal structure of beta-glucosidase from Thermoanaerobacterium saccharolyticum (Data 2)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase
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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesThermoanaerobacterium saccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Molecules / Year: 2023
Title: The Conformational Change of the L3 Loop Affects the Structural Changes in the Substrate Binding Pocket Entrance of beta-Glucosidase.
Authors: Nam, K.H.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
C: Beta-glucosidase
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,94718
Polymers207,2294
Non-polymers71814
Water24,2661347
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9985
Polymers51,8071
Non-polymers1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area17020 Å2
MethodPISA
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9985
Polymers51,8071
Non-polymers1914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area16950 Å2
MethodPISA
3
C: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9754
Polymers51,8071
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area16970 Å2
MethodPISA
4
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9754
Polymers51,8071
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.213, 72.739, 97.385
Angle α, β, γ (deg.)92.48, 91.43, 95.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-glucosidase


Mass: 51807.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria)
Gene: Tsac_2208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3VXG7
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG 4000, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 90740 / % possible obs: 90.9 % / Redundancy: 3.7 % / CC1/2: 0.977 / Net I/σ(I): 9.02
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 4342 / CC1/2: 0.977

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.81 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 2010 2.23 %
Rwork0.1599 --
obs0.1608 90261 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14624 0 42 1347 16013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415131
X-RAY DIFFRACTIONf_angle_d0.6720476
X-RAY DIFFRACTIONf_dihedral_angle_d5.6921986
X-RAY DIFFRACTIONf_chiral_restr0.0462059
X-RAY DIFFRACTIONf_plane_restr0.0052643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.2441380.25584X-RAY DIFFRACTION80
2.16-2.210.23451300.19755967X-RAY DIFFRACTION84
2.21-2.280.25721550.1916444X-RAY DIFFRACTION93
2.28-2.350.26451430.18936524X-RAY DIFFRACTION92
2.35-2.440.24331390.18526441X-RAY DIFFRACTION92
2.44-2.530.27021440.17976441X-RAY DIFFRACTION92
2.53-2.650.21751460.16986408X-RAY DIFFRACTION91
2.65-2.790.23121400.16786053X-RAY DIFFRACTION86
2.79-2.960.19851520.17186283X-RAY DIFFRACTION90
2.96-3.190.20391490.16416608X-RAY DIFFRACTION94
3.19-3.510.18591480.15256563X-RAY DIFFRACTION93
3.51-4.020.16211450.13376230X-RAY DIFFRACTION89
4.02-5.070.15381380.12426399X-RAY DIFFRACTION91
5.07-100.1791430.15036306X-RAY DIFFRACTION90

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