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- PDB-2wcg: X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guan... -

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Basic information

Entry
Database: PDB / ID: 2wcg
TitleX-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site
ComponentsGLUCOSYLCERAMIDASE
KeywordsHYDROLASE / LIPID METABOLISM / GLUCOCEREBROSIDASE / MEMBRANE / LYSOSOME / GLUCOSIDASE / GLYCOPROTEIN / GAUCHER DISEASE / SPHINGOLIPID METABOLISM
Function / homology
Function and homology information


negative regulation of macromolecule metabolic process / steryl-beta-glucosidase activity / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / positive regulation of neuronal action potential / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process ...negative regulation of macromolecule metabolic process / steryl-beta-glucosidase activity / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / positive regulation of neuronal action potential / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / glucosylceramide catabolic process / lymphocyte migration / regulation of lysosomal protein catabolic process / scavenger receptor binding / glycolipid biosynthetic process / sphingosine biosynthetic process / response to thyroid hormone / autophagosome organization / glucosylceramidase activity / lysosomal protein catabolic process / microglial cell proliferation / glucosyltransferase activity / Glycosphingolipid catabolism / microglia differentiation / regulation of TOR signaling / lipid storage / positive regulation of type 2 mitophagy / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / pyramidal neuron differentiation / ceramide biosynthetic process / negative regulation of protein metabolic process / Transferases; Glycosyltransferases; Hexosyltransferases / response to dexamethasone / antigen processing and presentation / neuromuscular process / lysosome organization / beta-glucosidase activity / hematopoietic stem cell proliferation / response to testosterone / regulation of protein catabolic process / Association of TriC/CCT with target proteins during biosynthesis / motor behavior / negative regulation of interleukin-6 production / establishment of skin barrier / homeostasis of number of cells / regulation of macroautophagy / cholesterol metabolic process / negative regulation of protein-containing complex assembly / mitophagy / negative regulation of MAPK cascade / cell maturation / lysosomal lumen / cellular response to starvation / thymus development / determination of adult lifespan / protein catabolic process / respiratory electron transport chain / trans-Golgi network / regulation of membrane potential / response to estrogen / negative regulation of inflammatory response / autophagy / cellular response to tumor necrosis factor / T cell differentiation in thymus / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / immune response / signaling receptor binding / lysosomal membrane / endoplasmic reticulum / Golgi apparatus / 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
alpha-L-fucopyranose / Chem-MT5 / Glucosylceramidase / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBrumshtein, B. / Aguilar, M. / Garcia-Moreno, M.I. / Mellet, C.O. / Garcia-Fernandez, J.M. / Silman, I. / Shaaltiel, Y. / Aviezer, D. / Sussman, J.L. / Futerman, A.H.
CitationJournal: Chembiochem / Year: 2009
Title: 6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.
Authors: Brumshtein, B. / Aguilar-Moncayo, M. / Garcia-Moreno, M.I. / Ortiz Mellet, C. / Garcia Fernandez, J.M. / Silman, I. / Shaaltiel, Y. / Aviezer, D. / Sussman, J.L. / Futerman, A.H.
History
DepositionMar 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / 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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 3.1Dec 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 3.2Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: GLUCOSYLCERAMIDASE
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,53622
Polymers113,1792
Non-polymers3,35820
Water13,349741
1
A: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,26811
Polymers56,5891
Non-polymers1,67910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GLUCOSYLCERAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,26811
Polymers56,5891
Non-polymers1,67910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.311, 96.827, 83.234
Angle α, β, γ (deg.)90.00, 104.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1509
2111B1508
1123A1 - 58
2123B1 - 58
1223A64 - 311
2223B64 - 311
1323A320 - 344
2323B320 - 344
1423A351 - 395
2423B351 - 395
1523A400 - 497
2523B400 - 497
1131A1499 - 1502
2131B1498 - 1501

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUCOSYLCERAMIDASE


Mass: 56589.285 Da / Num. of mol.: 2 / Fragment: RESIDUES 40-536
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: DAUCUS CAROTA (carrot)
References: UniProt: B2R6A7, UniProt: P04062*PLUS, glucosylceramidase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 757 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MT5 / N-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5-A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM


Mass: 316.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N3O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsN'-OCTYL(CYCLIC GUANIDINE)-NOJIRIMYCIN (MT5): ALIPHATIC TAIL IS INVISIBLE IN ELECTRON DENSITY AND, ...N'-OCTYL(CYCLIC GUANIDINE)-NOJIRIMYCIN (MT5): ALIPHATIC TAIL IS INVISIBLE IN ELECTRON DENSITY AND, THEREFORE, IS ABSENT FROM THE STRUCTURE
Sequence detailsTWO ADDITIONAL AMINO ACIDS AT THE N-TERMINAL (EF) AND SIX AMINO ACIDS AT THE C-TERMINAL (LLVDTM)

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.2M (NH4)2SO4, 0.1M TRIS PH 6.5, 25%(W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2008
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.29→20 Å / Num. obs: 52146 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.41 / % possible all: 89.6

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Processing

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

2v3f


Resolution: 2.3→19.74 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.402 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALIPHATIC TAIL OF THE INHIBITOR WAS NOT MODELED INTO THE STRUCTURE. FLEXIBLE REGIONS THAT SHOW NO CLEAR ELECTRON DENSITY WERE NOT MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2346 5 %RANDOM
Rwork0.135 ---
obs0.138 44184 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7743 0 188 741 8672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228158
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.96511142
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89423.353346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.364151218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2911540
X-RAY DIFFRACTIONr_chiral_restr0.1160.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216168
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_it0.8451.54933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59927956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71433225
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2724.53186
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A14tight positional0.040.05
12B14tight positional0.040.05
21A1872tight positional0.060.05
22B1872tight positional0.060.05
31A49tight positional0.060.05
32B49tight positional0.060.05
21A1759loose positional0.15
22B1759loose positional0.15
11A14tight thermal0.270.5
12B14tight thermal0.270.5
21A1872tight thermal0.190.5
22B1872tight thermal0.190.5
31A49tight thermal0.140.5
32B49tight thermal0.140.5
21A1759loose thermal0.2210
22B1759loose thermal0.2210
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 160 -
Rwork0.166 3158 -
obs--96.71 %

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