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- PDB-2vt0: X-ray structure of a conjugate with conduritol-beta-epoxide of ac... -

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Basic information

Entry
Database: PDB / ID: 2vt0
TitleX-ray structure of a conjugate with conduritol-beta-epoxide of acid-beta-glucosidase overexpressed in cultured plant cells
ComponentsGLUCOSYLCERAMIDASE
KeywordsHYDROLASE / ALTERNATIVE INITIATION / SPHINGOLIPID METABOLISM / ISRAEL STRUCTURAL PROTEOMICS CENTER / DISEASE MUTATION / GLUCOCEREBROSIDASE / PHARMACEUTICAL / GAUCHER DISEASE / LIPID METABOLISM / GLUCOSIDASE / GLYCOSIDASE / POLYMORPHISM / GLYCOPROTEIN / ISPC / MEMBRANE / CEREZYME / LYSOSOME / STRUCTURAL GENOMICS / ALTERNATIVE SPLICING
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 / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / lysosome organization / Transferases; Glycosyltransferases; Hexosyltransferases / regulation of protein catabolic process / response to dexamethasone / regulation of TOR signaling / 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 / cellular response to tumor necrosis factor / trans-Golgi network / 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
(1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL / Lysosomal acid glucosylceramidase / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBrumshtein, B. / Greenblatt, H.M. / Shaaltiel, Y. / Aviezer, D. / Silman, I. / Futerman, A.H. / Sussman, J.L.
CitationJournal: Biol.Chem. / Year: 2008
Title: Acid Beta-Glucosidase: Insights from Structural Analysis and Relevance to Gaucher Disease Therapy.
Authors: Kacher, Y. / Brumshtein, B. / Boldin-Adamsky, S. / Toker, L. / Shainskaya, A. / Silman, I. / Sussman, J.L. / Futerman, A.H.
History
DepositionMay 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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_atom_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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 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", "BC" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC", "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

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Assembly

Deposited unit
A: GLUCOSYLCERAMIDASE
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,80316
Polymers113,1792
Non-polymers2,62414
Water8,359464
1
A: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0799
Polymers56,5891
Non-polymers1,4898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7247
Polymers56,5891
Non-polymers1,1356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.184, 96.884, 83.171
Angle α, β, γ (deg.)90.00, 103.73, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAHISHISAA1 - 1623 - 164
21ALAALAHISHISBB1 - 1623 - 164
12LEULEUMETMETAA167 - 450169 - 452
22LEULEUMETMETBB167 - 450169 - 452
13PROPROARGARGAA452 - 496454 - 498
23PROPROARGARGBB452 - 496454 - 498

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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 / GLUCOSIDASE


Mass: 56589.285 Da / Num. of mol.: 2 / Fragment: TIM BARREL GLUCOSIDASE, RESIDUES 40-536
Source method: isolated from a genetically manipulated source
Details: THE ENZYME IS COVALENTLY INHIBITED BY CBE / Source: (gene. exp.) HOMO SAPIENS (human) / Organ: LYSOSOME / Production host: DAUCUS CAROTA (carrot)
References: UniProt: Q9BDT0, UniProt: P04062*PLUS, glucosylceramidase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[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-1a_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
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 476 molecules

#4: Chemical ChemComp-CBU / (1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6-HEXOL


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsCBU IS THE COVALENTLY BOUND FORM OF CONDURITOL-BETA-EPOXIDE, ONLY STEREOISOMER WAS EXPERIMENTALLY ...CBU IS THE COVALENTLY BOUND FORM OF CONDURITOL-BETA-EPOXIDE, ONLY STEREOISOMER WAS EXPERIMENTALLY OBSERVED IN THE STRUCTURE

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growMethod: microbatch / pH: 6.5
Details: 0.2M AMMONIUM SULFATE; 0.1M TRIS PH 6.5; 25% W/V PEG 3350; CRYSTALLIZATION UNDER OIL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 3, 2008
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 59355 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.73 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V3F

2v3f


Resolution: 2.15→19.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.52 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 27-31 ON CHAIN A AND 27-33 ON CHAIN B ARE NOT VISIBLE IN ELECTRON DENSITY, HENCE ARE MISSING
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2838 5.1 %RANDOM
Rwork0.152 ---
obs0.154 53238 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.18 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7723 0 159 464 8346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0228119
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.96311089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2285979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58323.381349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.264151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5741540
X-RAY DIFFRACTIONr_chiral_restr0.140.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216145
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0111.54907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76527912
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it333212
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5434.53177
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

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1936tight positional0.060.05
2B1936tight positional0.060.05
1A1848medium positional0.10.5
2B1848medium positional0.10.5
1A1936tight thermal0.270.5
2B1936tight thermal0.270.5
1A1848medium thermal0.322
2B1848medium thermal0.322
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 201
Rwork0.2 3474

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