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- PDB-5npf: Crystal structure of txGH116 (beta-glucosidase from Thermoanaerob... -

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Basic information

Entry
Database: PDB / ID: 5npf
TitleCrystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with beta Cyclophellitol Cyclosulfate probe ME594
ComponentsGlucosylceramidase
KeywordsHYDROLASE
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
Chem-945 / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWu, L. / Offen, W.A. / Breen, I.Z. / Davies, G.J.
CitationJournal: ACS Cent Sci / Year: 2017
Title: 1,6-Cyclophellitol Cyclosulfates: A New Class of Irreversible Glycosidase Inhibitor.
Authors: Artola, M. / Wu, L. / Ferraz, M.J. / Kuo, C.L. / Raich, L. / Breen, I.Z. / Offen, W.A. / Codee, J.D.C. / van der Marel, G.A. / Rovira, C. / Aerts, J.M.F.G. / Davies, G.J. / Overkleeft, H.S.
History
DepositionApr 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _software.classification
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,84416
Polymers91,7231
Non-polymers1,12115
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, single peak in gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint25 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.180, 53.810, 83.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Glucosylceramidase / txGH116


Mass: 91723.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (bacteria)
Gene: Thexy_2211 / Production host: Escherichia coli (E. coli) / References: UniProt: F6BL85, glucosylceramidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-945 / [(1~{R},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate


Mass: 274.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O9S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.38→53.81 Å / Num. obs: 163829 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.03 / Net I/σ(I): 15.1
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.968 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 11276 / CC1/2: 0.508 / Rpim(I) all: 0.59 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bvu

5bvu


Resolution: 1.38→51.57 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.028 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 8245 5 %RANDOM
Rwork0.12545 ---
obs0.12724 155502 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å2-0 Å2
2---1.53 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.38→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6185 0 69 567 6821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026687
X-RAY DIFFRACTIONr_bond_other_d0.0020.025956
X-RAY DIFFRACTIONr_angle_refined_deg1.741.9389069
X-RAY DIFFRACTIONr_angle_other_deg1.022313932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54825.361319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.168151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6291512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2908
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027520
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3581.643186
X-RAY DIFFRACTIONr_mcbond_other2.3521.6393185
X-RAY DIFFRACTIONr_mcangle_it2.8842.4774022
X-RAY DIFFRACTIONr_mcangle_other2.8852.4774023
X-RAY DIFFRACTIONr_scbond_it2.911.9513501
X-RAY DIFFRACTIONr_scbond_other2.9011.953498
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3932.7855046
X-RAY DIFFRACTIONr_long_range_B_refined3.9420.2398006
X-RAY DIFFRACTIONr_long_range_B_other3.94220.248007
X-RAY DIFFRACTIONr_rigid_bond_restr2.468312643
X-RAY DIFFRACTIONr_sphericity_free33.1055396
X-RAY DIFFRACTIONr_sphericity_bonded16.98512644
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 577 -
Rwork0.359 10686 -
obs--93.25 %

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