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- PDB-7dkt: Crystal structure of TxGH116 E441A nucleophile mutant from Thermo... -

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Basic information

Entry
Database: PDB / ID: 7dkt
TitleCrystal structure of TxGH116 E441A nucleophile mutant from Thermoanaerobacterium xylanolyticum with alpha-glucosyl fluoride
Componentsbeta-glucosidase
KeywordsHYDROLASE / beta-glucosidase / nucleophile mutant
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
Glycosyl-hydrolase family 116, catalytic region / Beta-glucosidase GBA2-type / Glycosyl-hydrolase family 116, N-terminal / : / Glycosyl-hydrolase family 116, catalytic region / beta-glucosidase 2, glycosyl-hydrolase family 116 N-term / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
alpha-D-glucopyranosyl fluoride / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Other privateThailand Research Fund Thailand
Other privateSuranaree University of Technology e Higher Education Commission under NRU Project of Thailand Thailand
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structural basis for transglycosylation in glycoside hydrolase family GH116 glycosynthases.
Authors: Pengthaisong, S. / Hua, Y. / Ketudat Cairns, J.R.
History
DepositionNov 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)93,15616
Polymers91,7361
Non-polymers1,41915
Water11,746652
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-12 kcal/mol
Surface area25860 Å2
Unit cell
Length a, b, c (Å)177.049, 54.689, 83.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein beta-glucosidase


Mass: 91736.148 Da / Num. of mol.: 1 / Mutation: E441A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, beta-glucosidase
#2: Sugar ChemComp-GLF / alpha-D-glucopyranosyl fluoride / 1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE / alpha-D-glucosyl fluoride / D-glucosyl fluoride / glucosyl fluoride


Type: D-saccharide / Mass: 182.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11FO5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1fluoroIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.21 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.14 M AMMONIUM SULFATE, 21% PEG 3350, 0.1 M MES, PH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→89 Å / Num. obs: 97660 / % possible obs: 99.6 % / Redundancy: 7.5 % / CC1/2: 0.985 / Net I/σ(I): 5.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7.5 % / Num. unique obs: 4756 / CC1/2: 0.83 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 1.65→88.52 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.746 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 4685 4.9 %RANDOM
Rwork0.1602 ---
obs0.1616 90318 96.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.65 Å2 / Biso mean: 16.882 Å2 / Biso min: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å20 Å2
2--0.35 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.65→88.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 91 652 6960
Biso mean--31.2 28.6 -
Num. residues----769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026538
X-RAY DIFFRACTIONr_bond_other_d0.0020.025975
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9418847
X-RAY DIFFRACTIONr_angle_other_deg0.917313812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2645781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47525.335313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.981151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9111512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021541
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 285 -
Rwork0.196 5393 -
all-5678 -
obs--79.15 %

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