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

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Basic information

Entry
Database: PDB / ID: 8wft
TitleCrystal structure of beta-glucosidase from Thermoanaerobacterium saccharolyticum (Data 1)
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glucosidase
Function / homology
Function and homology information


scopolin beta-glucosidase activity / 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: 1.9 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)208,30325
Polymers207,2294
Non-polymers1,07521
Water28,8061599
1
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0837
Polymers51,8071
Non-polymers2766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area17030 Å2
MethodPISA
2
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0606
Polymers51,8071
Non-polymers2535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17040 Å2
MethodPISA
3
C: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0996
Polymers51,8071
Non-polymers2925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16910 Å2
MethodPISA
4
D: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0606
Polymers51,8071
Non-polymers2535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.414, 72.831, 97.490
Angle α, β, γ (deg.)92.50, 91.28, 95.13
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1599 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
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: 1.9→50 Å / Num. obs: 123062 / % possible obs: 90.7 % / Redundancy: 3.7 % / CC1/2: 0.974 / Net I/σ(I): 10.78
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 6212 / CC1/2: 0.563

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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: 1.9→49.89 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 1986 1.62 %
Rwork0.1694 --
obs0.1698 122220 89.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14620 0 64 1599 16283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315111
X-RAY DIFFRACTIONf_angle_d0.63220431
X-RAY DIFFRACTIONf_dihedral_angle_d5.7581983
X-RAY DIFFRACTIONf_chiral_restr0.0442053
X-RAY DIFFRACTIONf_plane_restr0.0052633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.26651330.23668028X-RAY DIFFRACTION84
1.95-20.24541440.2158658X-RAY DIFFRACTION90
2-2.060.24251310.20118653X-RAY DIFFRACTION90
2.06-2.130.23921450.19938493X-RAY DIFFRACTION88
2.13-2.20.221230.18928051X-RAY DIFFRACTION84
2.2-2.290.22721530.18618834X-RAY DIFFRACTION92
2.29-2.40.2441420.18178761X-RAY DIFFRACTION92
2.4-2.520.20931470.17748802X-RAY DIFFRACTION92
2.52-2.680.19531450.17258678X-RAY DIFFRACTION91
2.68-2.890.2111400.17068262X-RAY DIFFRACTION86
2.89-3.180.21191580.17068991X-RAY DIFFRACTION94
3.18-3.640.1681400.15338834X-RAY DIFFRACTION92
3.64-4.580.15011380.13628478X-RAY DIFFRACTION88
4.58-49.890.15351470.14968711X-RAY DIFFRACTION91

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