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- PDB-7e5j: Crystal structure of beta-glucosidase from Thermoanaerobacterium ... -

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Basic information

Entry
Database: PDB / ID: 7e5j
TitleCrystal structure of beta-glucosidase from Thermoanaerobacterium saccharolyticum
ComponentsBeta-glucosidase
KeywordsHYDROLASE / native / Tris / glucosidase / beta-glucosidase / Thermoanaerobacterium saccharolyticum
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 / molecular replacement / Resolution: 1.71 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: Molecules / Year: 2022
Title: Biochemical and Structural Analysis of a Glucose-Tolerant beta-Glucosidase from the Hemicellulose-Degrading Thermoanaerobacterium saccharolyticum.
Authors: Kim, I.J. / Bornscheuer, U.T. / Nam, K.H.
History
DepositionFeb 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1265
Polymers51,9351
Non-polymers1914
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.139, 71.293, 99.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-glucosidase


Mass: 51935.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485) (bacteria)
Strain: DSM 8691 / JW/SL-YS485 / Gene: Tsac_2208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3VXG7, beta-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, PEG 3350, 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 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 50041 / % possible obs: 98.4 % / Redundancy: 5.4 % / CC1/2: 0.979 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.059 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 2429 / CC1/2: 0.663 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZ6

4hz6


Resolution: 1.71→49.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.155 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1823 2000 4 %RANDOM
Rwork0.141 ---
obs0.1427 48003 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.03 Å2 / Biso mean: 17.581 Å2 / Biso min: 8.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.67 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.71→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 11 591 4266
Biso mean--27.75 33.1 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133836
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173492
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.6355200
X-RAY DIFFRACTIONr_angle_other_deg1.461.5898053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16623.213221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5331518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02942
LS refinement shellResolution: 1.71→1.751 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 137 -
Rwork0.231 3291 -
obs--92.2 %

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