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- PDB-8r06: CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BE... -

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Basic information

Entry
Database: PDB / ID: 8r06
TitleCRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLANOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE
ComponentsGlucosylceramidase
KeywordsHYDROLASE / Glucosylceramidase
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-PO8 / Glucosylceramidase
Similarity search - Component
Biological speciesThermoanaerobacterium xylanolyticum LX-11 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOffen, W.A. / Davies, G.J. / Breen, I.Z.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2012-AdG-322942European Union
CitationJournal: JACS / Year: 2017
Title: CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLOLYTICUM GH116 BETA-GLUCOSIDASE WITH A COVALENTLY BOUND CYCLOPHELLITOL AZIRIDINE
Authors: Lahav, D. / Liu, B. / van den Berg, R.J.B.H.N. / van den Nieuwendijk, A.M.C.H. / Wennekes, T. / Ghisaidoobe, A.T. / Breen, I. / Ferraz, M.J. / Kuo, C.-L. / Wu, L. / Geurink, P.P. / Ovaa, H. ...Authors: Lahav, D. / Liu, B. / van den Berg, R.J.B.H.N. / van den Nieuwendijk, A.M.C.H. / Wennekes, T. / Ghisaidoobe, A.T. / Breen, I. / Ferraz, M.J. / Kuo, C.-L. / Wu, L. / Geurink, P.P. / Ovaa, H. / van der Marel, G.A. / van der Stelt, M. / Boot, R.G. / Davies, G.J. / Aerts, J.M.F.G. / Overkleeft, H.S.
History
DepositionOct 30, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionNov 22, 2023ID: 5NCX
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)92,2486
Polymers91,7941
Non-polymers4545
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mixture of monomer and dimer in SEC MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-22 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.621, 83.295, 177.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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
Details: C-terminal his-tagged construct without first 18 amino acids
Source: (gene. exp.) Thermoanaerobacterium xylanolyticum LX-11 (bacteria)
Gene: Thexy_2211 / Production host: Escherichia coli (E. coli) / References: UniProt: F6BL85

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-PO8 / (1~{R},2~{S},3~{S},4~{S},5~{R},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol


Mass: 194.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H16NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.2 M ammonium sulfate, 20% PEG 3350, 0.1M BisTris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→60.81 Å / Num. obs: 87708 / % possible obs: 99.5 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.044 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.002 / Num. unique obs: 4432 / CC1/2: 0.578 / Rpim(I) all: 0.456

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→60.81 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.048 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LIGAND IS COVALENTLY BOUND, ALTHOUGH THE DIFFERENCE DENSITY MAY INDICATE A SMALL PROPORTION OF AN UNREACTED FORM OF THE LIGAND, NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LIGAND IS COVALENTLY BOUND, ALTHOUGH THE DIFFERENCE DENSITY MAY INDICATE A SMALL PROPORTION OF AN UNREACTED FORM OF THE LIGAND, NOT MODELLED, ALSO PRESENT IN THE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.18877 4366 5 %RANDOM
Rwork0.15457 ---
obs0.15626 83288 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.7→60.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6213 0 26 371 6610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126436
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165824
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.8068722
X-RAY DIFFRACTIONr_angle_other_deg0.621.77113444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.1512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.656101062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021530
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_it1.8731.843087
X-RAY DIFFRACTIONr_mcbond_other1.8681.843086
X-RAY DIFFRACTIONr_mcangle_it2.7253.3033855
X-RAY DIFFRACTIONr_mcangle_other2.7253.3033856
X-RAY DIFFRACTIONr_scbond_it3.0812.1323349
X-RAY DIFFRACTIONr_scbond_other3.082.1333350
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7233.7454867
X-RAY DIFFRACTIONr_long_range_B_refined5.57117.997418
X-RAY DIFFRACTIONr_long_range_B_other5.57117.997419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 300 -
Rwork0.269 6074 -
obs--99.02 %

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