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- PDB-5o0s: Crystal structure of txGH116 (beta-glucosidase from Thermoanaerob... -

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Basic information

Entry
Database: PDB / ID: 5o0s
TitleCrystal structure of txGH116 (beta-glucosidase from Thermoanaerobacterium xylolyticum) in complex with unreacted beta Cyclophellitol Cyclosulfate probe ME711
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-9FQ / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsWu, L. / Offen, W.A. / Breen, I.Z. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilErC-2012-AdG-322942 United Kingdom
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
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation / citation_author
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
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

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Assembly

Deposited unit
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,22212
Polymers90,3671
Non-polymers85511
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, single peak from gel filtration at expected size for monomeric protein. Gives single band on SDS page.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint16 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.170, 53.731, 83.138
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


Mass: 90366.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (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.: 9 / 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-9FQ / (3~{a}~{S},4~{R},5~{S},6~{R},7~{R},7~{a}~{R})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydrobenzo[d][1,3,2]dioxathiole-4,5,6-triol


Mass: 256.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O8S
#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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM MES pH 6.5 0.2 M Ammonium Sulfate 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.16→59.39 Å / Num. obs: 275502 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.04 / Net I/σ(I): 11.3
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 2.09 / Mean I/σ(I) obs: 1 / Num. unique obs: 13526 / CC1/2: 0.515 / Rpim(I) all: 1.14 / % possible all: 100

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Processing

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

5fjs


Resolution: 1.16→59.39 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.62 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16298 13813 5 %Same as 5NPF
Rwork0.13887 ---
obs0.14009 261588 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å2-0 Å2
2---1.65 Å20 Å2
3---2.02 Å2
Refinement stepCycle: 1 / Resolution: 1.16→59.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 53 567 6845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026704
X-RAY DIFFRACTIONr_bond_other_d0.0020.025962
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9399098
X-RAY DIFFRACTIONr_angle_other_deg1.031313937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5435820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98225.298319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05151139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5921513
X-RAY DIFFRACTIONr_chiral_restr0.1170.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027553
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021412
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_it1.7781.6053202
X-RAY DIFFRACTIONr_mcbond_other1.7581.6043199
X-RAY DIFFRACTIONr_mcangle_it2.2462.4254040
X-RAY DIFFRACTIONr_mcangle_other2.2482.4254041
X-RAY DIFFRACTIONr_scbond_it2.3011.8293502
X-RAY DIFFRACTIONr_scbond_other2.3011.8283499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7032.6415057
X-RAY DIFFRACTIONr_long_range_B_refined6.57519.7948103
X-RAY DIFFRACTIONr_long_range_B_other6.57519.7948104
X-RAY DIFFRACTIONr_rigid_bond_restr2.853312666
X-RAY DIFFRACTIONr_sphericity_free30.8545363
X-RAY DIFFRACTIONr_sphericity_bonded17.621512662
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 1065 -
Rwork0.285 19142 -
obs--99.91 %

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