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- PDB-8jbo: Crystal structure of TxGH116 from Thermoanaerobacterium xylanolyt... -

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Basic information

Entry
Database: PDB / ID: 8jbo
TitleCrystal structure of TxGH116 from Thermoanaerobacterium xylanolyticum with isofagomine
ComponentsGlucosylceramidase
KeywordsHYDROLASE / TxGH116 / beta-glucosidase / acid/base mutant / Thermoanaerobacterium xylanolyticum / cellobiose
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / carbohydrate metabolic process / membrane / metal ion binding
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
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPengthaisong, S. / Ketudat Cairns, J.R.
Funding support Thailand, 3items
OrganizationGrant numberCountry
Other governmentThailand Research Fund Thailand
Other governmentSuranaree University of Technology Thailand
Other governmentThailand Science Research and Innovation Thailand
CitationJournal: Chem.Biol.Interact. / Year: 2023
Title: Structural basis for inhibition of a GH116 beta-glucosidase and its missense mutants by GBA2 inhibitors: Crystallographic and quantum chemical study.
Authors: Meelua, W. / Thinkumrob, N. / Saparpakorn, P. / Pengthaisong, S. / Hannongbua, S. / Ketudat Cairns, J.R. / Jitonnom, J.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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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)185,82729
Polymers183,4462
Non-polymers2,38127
Water17,421967
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,93315
Polymers91,7231
Non-polymers1,21014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89314
Polymers91,7231
Non-polymers1,17013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.791, 164.399, 179.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1 / Auth seq-ID: 31 - 801 / Label seq-ID: 15 - 785

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999753, -0.008936, -0.020366), (-0.008089, 0.999114, -0.041306), (0.020717, -0.041131, -0.998939)2.12318, 1.87405, 92.591469

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glucosylceramidase /


Mass: 91723.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Strain: LX-11 / Gene: Thexy_2211 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F6BL85

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Non-polymers , 5 types, 994 molecules

#2: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 967 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M AMMONIUM SULFATE, 23% 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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50.01 Å / Num. obs: 109281 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 26.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 5192 / CC1/2: 0.884 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.592 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.193 5466 5 %RANDOM
Rwork0.155 ---
obs0.1569 103720 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.52 Å2 / Biso mean: 22.149 Å2 / Biso min: 8.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å20 Å2-0 Å2
2---0.62 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12434 0 151 967 13552
Biso mean--37.24 30.06 -
Num. residues----1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212978
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211862
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.93917554
X-RAY DIFFRACTIONr_angle_other_deg0.987327399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4751544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23425.282621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.898152163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931524
X-RAY DIFFRACTIONr_chiral_restr0.0910.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214704
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023066
Refine LS restraints NCSNumber: 12071 / Type: TIGHT THERMAL / Rms dev position: 2 Å / Weight position: 0.5
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.24 374 -
Rwork0.206 6931 -
obs--90.77 %

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