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- PDB-2jfe: The crystal structure of human cytosolic beta-glucosidase -

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Basic information

Entry
Database: PDB / ID: 2jfe
TitleThe crystal structure of human cytosolic beta-glucosidase
ComponentsCYTOSOLIC BETA-GLUCOSIDASE
KeywordsHYDROLASE / HUMAN CYTOSOLIC BETA-GLUCOSIDASE / FAMILY GH1 BETA- GLUCOSIDASE / ALTERNATIVE SPLICING / FLAVONOID-GLYCOSIDASE / GLYCOSIDASE / POLYMORPHISM
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 / glycosphingolipid catabolic process / glucosylceramide 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 / glycosphingolipid catabolic process / glucosylceramide catabolic process / glucosylceramidase activity / glycoside catabolic process / : / oligosaccharide catabolic process / Glycosphingolipid catabolism / beta-glucosidase / beta-galactosidase activity / beta-glucosidase 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
Cytosolic beta-glucosidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCzjzek, M. / Tribolo, S. / Berrin, J.G. / Kroon, P.A. / Juge, N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of Human Cytosolic Beta-Glucosidase Unravels the Substrate Aglycone Specificity of a Family 1 Glycoside Hydrolase
Authors: Tribolo, S. / Berrin, J.G. / Kroon, P.A. / Czjzek, M. / Juge, N.
History
DepositionJan 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: CYTOSOLIC BETA-GLUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1602
Polymers53,7351
Non-polymers4241
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)90.479, 90.479, 127.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CYTOSOLIC BETA-GLUCOSIDASE / HUMAN CYTOSOLIC BETA-GLUCOSIDASE


Mass: 53735.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: CYTOSOLIC / Plasmid: PHIL-S1/CBG-1 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): (HIS4)/GS115 / References: UniProt: Q9H227, beta-glucosidase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growpH: 6.5
Details: CRYSTALS GREW WITHIN SEVERAL DAYS IN THE CRYSTALLIZATION TRIAL CONTAINING 0.2 M AMMONIUM SULPHATE, MES BUFFER AT PH 6.5 AND 30 % (W/V) POLYETHYLENEGLYCOL-MONOMETHYLETHER (PEG-MME) 5500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 17144 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 10.6
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V02

1v02


Resolution: 2.7→42.64 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.858 / SU B: 6.378 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 1.355 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28 865 5 %RANDOM
Rwork0.197 ---
obs0.201 16273 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3725 0 28 158 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.9425264
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9565458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19224.346191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.64615613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5471515
X-RAY DIFFRACTIONr_chiral_restr0.120.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023009
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.22168
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22642
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2210
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.52337
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09723686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52231798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3364.51578
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.333 72
Rwork0.166 1170

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