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- PDB-5ost: Beta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in ... -

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Basic information

Entry
Database: PDB / ID: 5ost
TitleBeta-glucosidase from Thermoanaerobacterium xylolyticum GH116 in complex with Gluco-1H-imidazole
ComponentsGlucosylceramidase
KeywordsHYDROLASE
Function / homology
Function and homology information


glucosylceramidase / glucosylceramide catabolic process / glucosylceramidase activity / beta-glucosidase activity / carbohydrate metabolic process / 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-AEZ / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDavies, G.J. / Offen, W.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Gluco-1 H-imidazole: A New Class of Azole-Type beta-Glucosidase Inhibitor.
Authors: Schroder, S.P. / Wu, L. / Artola, M. / Hansen, T. / Offen, W.A. / Ferraz, M.J. / Li, K.Y. / Aerts, J.M.F.G. / van der Marel, G.A. / Codee, J.D.C. / Davies, G.J. / Overkleeft, H.S.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2May 9, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 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)92,70816
Polymers91,7941
Non-polymers91415
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-34 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.617, 54.090, 83.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-910-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glucosylceramidase


Mass: 91794.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum (strain ATCC 49914 / DSM 7097 / LX-11) (bacteria)
Gene: Thexy_2211 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6BL85, glucosylceramidase

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AEZ / (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol


Mass: 200.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, ammonium sulphate, Bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→88.76 Å / Num. obs: 36706 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.949 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.126 / Net I/σ(I): 5.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.63 / Mean I/σ(I) obs: 2 / Num. unique obs: 3567 / CC1/2: 0.748 / Rpim(I) all: 0.64 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BVU

5bvu


Resolution: 2.1→88.97 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.63 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING. RESIDUES 429-431 ARE NOT MODELLED POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25094 2286 4.9 %RANDOM
Rwork0.19978 ---
obs0.20224 44762 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.56 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å2-0 Å20 Å2
2--2.78 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.1→88.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 52 268 6420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026328
X-RAY DIFFRACTIONr_bond_other_d0.0020.025512
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9338581
X-RAY DIFFRACTIONr_angle_other_deg1.038312817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65825.196306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.442151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1031513
X-RAY DIFFRACTIONr_chiral_restr0.1060.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021346
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_it1.912.5753050
X-RAY DIFFRACTIONr_mcbond_other1.912.5753049
X-RAY DIFFRACTIONr_mcangle_it2.7863.8583809
X-RAY DIFFRACTIONr_mcangle_other2.7853.8583810
X-RAY DIFFRACTIONr_scbond_it1.9562.6613278
X-RAY DIFFRACTIONr_scbond_other1.9562.6613279
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8943.9424773
X-RAY DIFFRACTIONr_long_range_B_refined4.30429.4817526
X-RAY DIFFRACTIONr_long_range_B_other4.30329.4817527
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 170 -
Rwork0.276 3255 -
obs--97.77 %

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