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- PDB-7f1n: Beta-Glucosidase -

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Basic information

Entry
Database: PDB / ID: 7f1n
TitleBeta-Glucosidase
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / 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 speciesThermofilum sp. ex4484_79 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14000368188 Å
AuthorsAnke, C.
CitationJournal: Front Microbiol / Year: 2021
Title: Structural and Catalytic Characterization of TsBGL, a beta-Glucosidase From Thermofilum sp. ex4484_79.
Authors: Chen, A. / Wang, D. / Ji, R. / Li, J. / Gu, S. / Tang, R. / Ji, C.
History
DepositionJun 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
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

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,4874
Polymers117,4382
Non-polymers492
Water8,557475
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.720, 62.210, 112.450
Angle α, β, γ (deg.)90.000, 98.508, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-galactosidase


Mass: 58718.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermofilum sp. ex4484_79 (archaea) / Gene: B6U94_07015 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A256XQM7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 30% (v/v) MPD, 100mM Imidazole/Hydrochloric PH6, 5200mM Ammonium sulfate, 10% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.14→111.213 Å / Num. obs: 56997 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.7434634222 Å2 / CC1/2: 0.857 / Net I/σ(I): 3.6
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 3988 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qvb

1qvb


Resolution: 2.14000368188→111.212511998 Å / SU ML: 0.229128423089 / Cross valid method: NONE / σ(F): 1.38324839426 / Phase error: 26.38210846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252517316067 2816 4.94390702084 %
Rwork0.209689983167 54143 -
obs0.211842610613 56959 97.9148043732 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.9701223454 Å2
Refinement stepCycle: LAST / Resolution: 2.14000368188→111.212511998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8122 0 2 475 8599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003003412092438352
X-RAY DIFFRACTIONf_angle_d0.62260152630611346
X-RAY DIFFRACTIONf_chiral_restr0.04579971368561205
X-RAY DIFFRACTIONf_plane_restr0.003897320561449
X-RAY DIFFRACTIONf_dihedral_angle_d22.55950254484921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.140004-2.17690.2670731807281400.2302978028612538X-RAY DIFFRACTION93.4403349616
2.1769-2.21650.2763194117491410.2279583841392614X-RAY DIFFRACTION94.9018256976
2.2165-2.25910.3290527879321520.2382325611622637X-RAY DIFFRACTION96.8402777778
2.2591-2.30520.2942147501511270.2399963408282696X-RAY DIFFRACTION97.1104231166
2.3052-2.35540.2417869624751510.2264663050512511X-RAY DIFFRACTION92.6880222841
2.3554-2.41020.2674849457341230.2273410985172680X-RAY DIFFRACTION97.3940236275
2.4102-2.47040.2730920468571510.220322824442733X-RAY DIFFRACTION98.396451723
2.4704-2.53720.2738197754831230.2236683635942705X-RAY DIFFRACTION98.6741102582
2.5372-2.61190.2810455770791410.2248801589892706X-RAY DIFFRACTION98.6828422877
2.6119-2.69620.2316152809941580.2304068571842692X-RAY DIFFRACTION98.6842105263
2.6962-2.79260.2843201135941290.2221285046222735X-RAY DIFFRACTION98.8267770876
2.7926-2.90440.2875953649161480.2254171051712746X-RAY DIFFRACTION99.0078686281
2.9044-3.03660.2656562442291460.2233914923852716X-RAY DIFFRACTION99.2371705964
3.0366-3.19670.2908724610721260.2209487019242766X-RAY DIFFRACTION99.1429550908
3.1967-3.3970.280267382641310.2066989955272762X-RAY DIFFRACTION99.2452830189
3.397-3.65930.2071537495841460.1951954535992775X-RAY DIFFRACTION99.21875
3.6593-4.02760.2441894557411600.1812371449942715X-RAY DIFFRACTION99.2063492063
4.0276-4.61040.2072121402631350.171473846142761X-RAY DIFFRACTION99.5873452545
4.6104-5.80860.2126082678431510.1940924548052809X-RAY DIFFRACTION99.3622020812

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