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- PDB-2v3e: acid-beta-glucosidase with N-nonyl-deoxynojirimycin -

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Basic information

Entry
Database: PDB / ID: 2v3e
Titleacid-beta-glucosidase with N-nonyl-deoxynojirimycin
ComponentsGLUCOSYLCERAMIDASE
KeywordsHYDROLASE / ACID-BETA-GLUCOSIDASE / N-NONYL-DEOXYNOJIRIMYCINALTERNATIVE INITIATION / SPHINGOLIPID METABOLISM / N-NONYL-DEOXYNOJIRIMYCIN / GAUCHER DISEASE / DISEASE MUTATION / LIPID METABOLISM / POLYMORPHISM / GLYCOPROTEIN / PHARMACEUTICAL / ALTERNATIVE SPLICING / MEMBRANE / LYSOSOME / GLYCOSIDASE
Function / homology
Function and homology information


beta-glucoside catabolic process / steryl-beta-glucosidase activity / positive regulation of neuronal action potential / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / lysosomal protein catabolic process / glucosylceramidase / response to thyroid hormone / regulation of lysosomal protein catabolic process ...beta-glucoside catabolic process / steryl-beta-glucosidase activity / positive regulation of neuronal action potential / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / lysosomal protein catabolic process / glucosylceramidase / response to thyroid hormone / regulation of lysosomal protein catabolic process / scavenger receptor binding / glucosylceramide catabolic process / glycolipid biosynthetic process / sphingosine biosynthetic process / glucosylceramidase activity / glucosyltransferase activity / Glycosphingolipid catabolism / ceramide biosynthetic process / response to pH / regulation of TOR signaling / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / lysosome organization / Transferases; Glycosyltransferases; Hexosyltransferases / response to dexamethasone / beta-glucosidase activity / response to testosterone / negative regulation of interleukin-6 production / Association of TriC/CCT with target proteins during biosynthesis / establishment of skin barrier / cholesterol metabolic process / negative regulation of MAPK cascade / regulation of macroautophagy / lysosomal lumen / cellular response to starvation / trans-Golgi network / cellular response to tumor necrosis factor / negative regulation of inflammatory response / response to estrogen / autophagy / lysosome / signaling receptor binding / lysosomal membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome
Similarity search - Function
Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Glycosyl hydrolase family 30, TIM-barrel domain / Glycosyl hydrolase family 30 TIM-barrel domain / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-NND / PHOSPHATE ION / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrumshtein, B. / Greenblatt, H.M. / Butters, T.D. / Shaaltiel, Y. / Aviezer, D. / Silman, I. / Futerman, A.H. / Sussman, J.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Complexes of N-Butyl- and N-Nonyl-Deoxynojirimycin Bound to Acid Beta-Glucosidase: Insights Into the Mechanism of Chemical Chaperone Action in Gaucher Disease.
Authors: Brumshtein, B. / Greenblatt, H.M. / Butters, T.D. / Shaaltiel, Y. / Aviezer, D. / Silman, I. / Futerman, A.H. / Sussman, J.L.
History
DepositionJun 17, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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 / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" AND "BC" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" AND "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSYLCERAMIDASE
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6349
Polymers113,1792
Non-polymers2,4557
Water18,0871004
1
A: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7064
Polymers56,5891
Non-polymers1,1173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9285
Polymers56,5891
Non-polymers1,3384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.998, 97.646, 82.348
Angle α, β, γ (deg.)90.00, 102.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A-1 - 27
2113B-1 - 27
1213A36 - 497
2213B36 - 497

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUCOSYLCERAMIDASE / BETA-GLUCOCEREBROSIDASE / ACID-BETA-GLUCOSIDASE / D-GLUCOSYL-N-ACYLSPHINGOSINE GLUCOHYDROLASE / ...BETA-GLUCOCEREBROSIDASE / ACID-BETA-GLUCOSIDASE / D-GLUCOSYL-N-ACYLSPHINGOSINE GLUCOHYDROLASE / ALGLUCERASE / IMIGLUCERASE


Mass: 56589.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NN-DNJ IN THE ACTIVE SITE / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: DAUCUS CAROTA (carrot) / References: UniProt: P04062, glucosylceramidase

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Sugars , 2 types, 3 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1008 molecules

#3: Chemical ChemComp-NND / (2R,3R,4R,5S)-2-(HYDROXYMETHYL)-1-NONYLPIPERIDINE-3,4,5-TRIOL / N-NONYL-DEOXYNOJIRIMYCIN


Mass: 289.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H31NO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1004 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsIN ADDITION TO THE NATIVE SEQUENCE OF HUMAN ACID-BETA-GLUCOSIDASE, THE MOLECULE HAS 2 AMINO ACIDS ...IN ADDITION TO THE NATIVE SEQUENCE OF HUMAN ACID-BETA-GLUCOSIDASE, THE MOLECULE HAS 2 AMINO ACIDS AT THE N-TERMINAL, AND 6 AMINO ACIDS AT THE C-TERMINAL

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M NH4COOCH3, 0.1 M HEPES PH 7.5, 25% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→23.62 Å / Num. obs: 59655 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.27
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 52.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V3F

2v3f


Resolution: 2→23.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.927 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3134 5 %RANDOM
Rwork0.16 ---
obs0.163 59655 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 162 1004 8995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.551.96611303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89951005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66423.445357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8711542
X-RAY DIFFRACTIONr_chiral_restr0.1070.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.24317
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25554
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8161.55133
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28928071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18133629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2584.53226
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1957tight positional0.060.05
1885loose positional0.265
1957tight thermal0.250.5
1885loose thermal1.4310
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 126
Rwork0.2 2454

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