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- PDB-7w2t: Crystal structure of TxGH116 E730Q mutant from Thermoanaerobacter... -

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Basic information

Entry
Database: PDB / ID: 7w2t
TitleCrystal structure of TxGH116 E730Q mutant from Thermoanaerobacterium xylanolyticum with glucose
ComponentsGlucosylceramidase
KeywordsHYDROLASE / TxGH116 / beta-glucosidase / mutant / Thermoanaerobacterium xylanolyticum / glucose
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
beta-D-glucopyranose / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHuang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Jitonnom, J. / Ketudat Cairns, J.R.
Funding support Thailand, 5items
OrganizationGrant numberCountry
Other governmentSuranaree University of Technology Thailand
Other governmentThailand Research Fund Thailand
Other governmentThailand Science Research and Innovation Thailand
Other governmentSynchrotron Light Research Institute (Public Organization) Thailand
Other governmentUniversity of Phayao Thailand
CitationJournal: Catalysts / Year: 2022
Title: Systematic Functional and Computational Analysis of Glucose-Binding Residues in Glycoside Hydrolase Family GH116.
Authors: Huang, M. / Pengthaisong, S. / Charoenwattanasatien, R. / Thinkumrob, N. / Jitonnom, J. / Ketudat Cairns, J.R.
History
DepositionNov 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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: Glucosylceramidase
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,26813
Polymers193,1832
Non-polymers1,08511
Water11,115617
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2728
Polymers96,5911
Non-polymers6817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area26040 Å2
MethodPISA
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9965
Polymers96,5911
Non-polymers4044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.377, 124.458, 174.263
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 Glucosylceramidase


Mass: 96591.445 Da / Num. of mol.: 2 / Mutation: E730Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11) (bacteria)
Strain: ATCC 49914 / DSM 7097 / LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85, glucosylceramidase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.29 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.15 M AMMONIUM SULFATE, 22% PEG 3000, 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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 86926 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 11.7
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8325 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 2.15→50.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.974 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 3983 4.9 %RANDOM
Rwork0.1526 ---
obs0.1551 77195 84.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.63 Å2 / Biso mean: 32.49 Å2 / Biso min: 13.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2--1.17 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.15→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12382 0 68 617 13067
Biso mean--42.85 36.34 -
Num. residues----1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212855
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211638
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.93517439
X-RAY DIFFRACTIONr_angle_other_deg0.995326836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79551553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24225.245612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21152102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0911524
X-RAY DIFFRACTIONr_chiral_restr0.0990.21777
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023064
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 93 -
Rwork0.193 2241 -
all-2334 -
obs--33.44 %

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