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- PDB-2zox: Crystal Structure of the Covalent Intermediate of Human Cytosolic... -

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Basic information

Entry
Database: PDB / ID: 2zox
TitleCrystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase
ComponentsCytosolic beta-glucosidase
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


glycosylceramidase activity / positive regulation of exo-alpha-sialidase activity / galactosylceramide catabolic process / glycosylceramide catabolic process / beta-glucoside catabolic process / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process / glycosphingolipid catabolic process ...glycosylceramidase activity / positive regulation of exo-alpha-sialidase activity / galactosylceramide catabolic process / glycosylceramide catabolic process / beta-glucoside catabolic process / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process / glycosphingolipid catabolic process / oligosaccharide catabolic process / glycoside catabolic process / glucosylceramidase activity / Glycosphingolipid catabolism / scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / beta-galactosidase activity / catalytic complex / protein stabilization / cytosol
Similarity search - Function
Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / OLEIC ACID / PALMITIC ACID / 4-nitrophenyl alpha-D-glucopyranoside / PHOSPHATE ION / Cytosolic beta-glucosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNoguchi, J. / Hayashi, Y. / Baba, Y. / Okino, N. / Kimura, M. / Ito, M. / Kakuta, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase
Authors: Noguchi, J. / Hayashi, Y. / Baba, Y. / Okino, N. / Kimura, M. / Ito, M. / Kakuta, Y.
History
DepositionJun 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,26310
Polymers53,7501
Non-polymers1,5129
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 82.529, 91.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytosolic beta-glucosidase / Cytosolic beta-glucosidase-like protein 1


Mass: 53750.402 Da / Num. of mol.: 1 / Mutation: E165Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA3, CBG, CBGL1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)codon plus RIL / References: UniProt: Q9H227, beta-glucosidase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-PNG / 4-nitrophenyl alpha-D-glucopyranoside / 4'-NITROPHENYL-ALPHA-D-GLUCOPYRANOSIDE / 4-nitrophenyl alpha-D-glucoside / 4-nitrophenyl D-glucoside / 4-nitrophenyl glucoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H15NO8
IdentifierTypeProgram
4'-nitrophenyl-a-D-glucopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 203 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#7: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl, 15% glycerol saturated concentration of pNP-Glc , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 39194 / Num. obs: 39194 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 19.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.428 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E9L

2e9l


Resolution: 1.9→30.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.451 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22578 1964 5 %RANDOM
Rwork0.19057 ---
obs0.19233 37229 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 101 196 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224011
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9545433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76224.337196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74815629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1751516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023089
X-RAY DIFFRACTIONr_nbd_refined0.190.21997
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.26
X-RAY DIFFRACTIONr_mcbond_it0.5571.52389
X-RAY DIFFRACTIONr_mcangle_it0.92523755
X-RAY DIFFRACTIONr_scbond_it1.38131900
X-RAY DIFFRACTIONr_scangle_it2.1654.51675
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 103 -
Rwork0.267 2287 -
obs--81.96 %

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