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- PDB-8xpc: Crystal structure of Tris-bound TsaBgl (DATA I) -

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Basic information

Entry
Database: PDB / ID: 8xpc
TitleCrystal structure of Tris-bound TsaBgl (DATA I)
Componentsbeta-glucosidase
KeywordsHYDROLASE / inhibitor / Tris / bgl
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 JW/SL-YS485 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A1A01050838 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Structural analysis of Tris binding in beta-glucosidases.
Authors: Nam, K.H.
History
DepositionJan 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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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)52,0287
Polymers51,7911
Non-polymers2376
Water10,413578
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 area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.752, 71.023, 98.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein beta-glucosidase


Mass: 51791.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium saccharolyticum JW/SL-YS485 (bacteria)
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.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, polyethylene glycol 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 PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 65751 / % possible obs: 98.5 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 16.89
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 3021 / CC1/2: 0.644

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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: 1.55→49.44 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1687 2000 3.05 %
Rwork0.1488 --
obs0.1494 65664 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 13 578 4255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063885
X-RAY DIFFRACTIONf_angle_d0.8965276
X-RAY DIFFRACTIONf_dihedral_angle_d5.733520
X-RAY DIFFRACTIONf_chiral_restr0.057532
X-RAY DIFFRACTIONf_plane_restr0.009687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.26081300.23094163X-RAY DIFFRACTION92
1.59-1.630.21951390.20314380X-RAY DIFFRACTION96
1.63-1.680.18641400.1894475X-RAY DIFFRACTION97
1.68-1.730.22771400.17864466X-RAY DIFFRACTION98
1.73-1.80.20691430.17254527X-RAY DIFFRACTION99
1.8-1.870.17761410.15524524X-RAY DIFFRACTION99
1.87-1.950.18571430.15064528X-RAY DIFFRACTION99
1.95-2.060.17391440.14794589X-RAY DIFFRACTION99
2.06-2.190.17821430.13564574X-RAY DIFFRACTION99
2.19-2.350.15571440.144576X-RAY DIFFRACTION99
2.35-2.590.15721460.14214638X-RAY DIFFRACTION100
2.59-2.970.17251460.14374647X-RAY DIFFRACTION100
2.97-3.740.13671470.12854689X-RAY DIFFRACTION100
3.74-49.440.14481540.13764888X-RAY DIFFRACTION100

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