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- PDB-9k72: Crystal structure of TsaBgl using merged datasets -

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Basic information

Entry
Database: PDB / ID: 9k72
TitleCrystal structure of TsaBgl using merged datasets
Componentsbeta-glucosidase
KeywordsHYDROLASE / beta-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: 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: Crystals / Year: 2024
Title: Application of Serial Crystallography for Merging Incomplete Macromolecular Crystallography Datasets.
Authors: Nam, K.H.
History
DepositionOct 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0287
Polymers51,7911
Non-polymers2376
Water8,359464
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 area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.210, 71.120, 99.490
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 (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: isolated from a natural source / Formula: C4H12NO3 / 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.: 464 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Tris-HCl, PEG4000, 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 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→100 Å / Num. obs: 67418 / % possible obs: 99.32 % / Redundancy: 14.3 % / CC1/2: 0.8547 / Net I/σ(I): 3.42
Reflection shellResolution: 1.55→1.6 Å / Num. unique obs: 7112 / CC1/2: 0.2974

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→57.86 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1475 2.2 %
Rwork0.2007 --
obs0.2014 67185 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→57.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 13 464 4141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073875
X-RAY DIFFRACTIONf_angle_d0.8495261
X-RAY DIFFRACTIONf_dihedral_angle_d5.633518
X-RAY DIFFRACTIONf_chiral_restr0.057531
X-RAY DIFFRACTIONf_plane_restr0.008684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.40381190.39795670X-RAY DIFFRACTION96
1.6-1.660.38591350.3215917X-RAY DIFFRACTION99
1.66-1.720.27211390.27655932X-RAY DIFFRACTION99
1.72-1.80.32311250.25585940X-RAY DIFFRACTION99
1.8-1.90.27021360.23855907X-RAY DIFFRACTION100
1.9-2.020.28721350.23915973X-RAY DIFFRACTION100
2.02-2.170.24691360.19455966X-RAY DIFFRACTION99
2.17-2.390.21191270.18375997X-RAY DIFFRACTION99
2.39-2.740.22261400.18196020X-RAY DIFFRACTION99
2.74-3.450.20981380.17776095X-RAY DIFFRACTION100
3.45-57.860.18881450.16756293X-RAY DIFFRACTION99

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