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- PDB-6tjk: Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane. -

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Basic information

Entry
Database: PDB / ID: 6tjk
TitleCrystal Structure of Recombinant GBA in Complex with Bis-Tris Propane.
ComponentsLysosomal acid glucosylceramidase
KeywordsHYDROLASE / beta-glucocerebrosidase / lysosomal glycoside hydrolase / GH30
Function / homology
Function and homology information


steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation ...steryl-beta-glucosidase activity / positive regulation of neuronal action potential / beta-glucoside catabolic process / cerebellar Purkinje cell layer formation / termination of signal transduction / galactosylceramidase / galactosylceramidase activity / glucosylceramidase / scavenger receptor binding / positive regulation of protein lipidation / lymphocyte migration / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / glucosylceramidase activity / sphingosine biosynthetic process / autophagosome organization / microglial cell proliferation / regulation of TOR signaling / glucosyltransferase activity / response to thyroid hormone / ceramide biosynthetic process / microglia differentiation / Glycosphingolipid catabolism / lipid storage / positive regulation of type 2 mitophagy / lipid glycosylation / brain morphogenesis / positive regulation of protein-containing complex disassembly / response to pH / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / pyramidal neuron differentiation / negative regulation of protein metabolic process / lysosome organization / motor behavior / Transferases; Glycosyltransferases; Hexosyltransferases / neuromuscular process / hematopoietic stem cell proliferation / antigen processing and presentation / response to dexamethasone / Association of TriC/CCT with target proteins during biosynthesis / response to testosterone / negative regulation of interleukin-6 production / homeostasis of number of cells / regulation of macroautophagy / establishment of skin barrier / negative regulation of protein-containing complex assembly / negative regulation of MAPK cascade / mitophagy / cell maturation / cholesterol metabolic process / lysosomal lumen / cellular response to starvation / respiratory electron transport chain / determination of adult lifespan / trans-Golgi network / negative regulation of inflammatory response / autophagy / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / T cell differentiation in thymus / neuron apoptotic process / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / lysosome / lysosomal membrane / signaling receptor binding / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsRowland, R.J. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: A baculoviral system for the production of human beta-glucocerebrosidase enables atomic resolution analysis.
Authors: Rowland, R.J. / Wu, L. / Liu, F. / Davies, G.J.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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 / pdbx_validate_symm_contact / struct_asym / struct_conn
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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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 3.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp / database_2 / entity / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref_seq
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 3.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 3.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Lysosomal acid glucosylceramidase
BBB: Lysosomal acid glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,67462
Polymers111,3182
Non-polymers6,35560
Water16,123895
1
AAA: Lysosomal acid glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,79229
Polymers55,6591
Non-polymers3,13328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Lysosomal acid glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,88133
Polymers55,6591
Non-polymers3,22232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.744, 156.222, 68.264
Angle α, β, γ (deg.)90.000, 102.473, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Lysosomal acid glucosylceramidase / Lysosomal acid GCase / Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / ...Lysosomal acid GCase / Acid beta-glucosidase / Alglucerase / Beta-glucocerebrosidase / Beta-GC / Cholesterol glucosyltransferase / SGTase / Cholesteryl-beta-glucosidase / D-glucosyl-N-acylsphingosine glucohydrolase / Imiglucerase


Mass: 55659.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA, GC, GLUC / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P04062, glucosylceramidase, Transferases; Glycosyltransferases; Hexosyltransferases, EC: 3.2.1.104

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Sugars , 2 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 3
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 , 4 types, 950 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 43
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H26N2O6 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.1 M bis-tris-propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→66.742 Å / Num. obs: 147746 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.057 / Net I/σ(I): 7.4
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 7162 / CC1/2: 0.336 / Rpim(I) all: 0.901

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q6K

6q6k


Resolution: 1.56→66.742 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.15 / SU B: 2.441 / SU ML: 0.079 / Average fsc free: 0.8514 / Average fsc work: 0.8613 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1985 7465 5.055 %
Rwork0.1646 140209 -
all0.166 --
obs-147674 96.714 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.553 Å2
Baniso -1Baniso -2Baniso -3
1-1.457 Å2-0 Å20.66 Å2
2---0.632 Å20 Å2
3----1.017 Å2
Refinement stepCycle: LAST / Resolution: 1.56→66.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7833 0 411 895 9139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138617
X-RAY DIFFRACTIONr_bond_other_d0.0040.0177814
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.67511685
X-RAY DIFFRACTIONr_angle_other_deg1.3941.58818134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47251036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46521.932414
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01915.0161280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9721546
X-RAY DIFFRACTIONr_chiral_restr0.0840.21098
X-RAY DIFFRACTIONr_chiral_restr_other0.1660.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021829
X-RAY DIFFRACTIONr_nbd_refined0.2140.21715
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.27473
X-RAY DIFFRACTIONr_nbtor_refined0.1710.24041
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.23523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2702
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1490.218
X-RAY DIFFRACTIONr_nbd_other0.2360.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.234
X-RAY DIFFRACTIONr_mcbond_it1.5792.1674062
X-RAY DIFFRACTIONr_mcbond_other1.5762.1674061
X-RAY DIFFRACTIONr_mcangle_it2.153.2465102
X-RAY DIFFRACTIONr_mcangle_other2.153.2465103
X-RAY DIFFRACTIONr_scbond_it2.372.4944555
X-RAY DIFFRACTIONr_scbond_other2.372.4944556
X-RAY DIFFRACTIONr_scangle_it3.3693.6256583
X-RAY DIFFRACTIONr_scangle_other3.3683.6266584
X-RAY DIFFRACTIONr_lrange_it4.78327.0449721
X-RAY DIFFRACTIONr_lrange_other4.77927.0439721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.3235440.32110176X-RAY DIFFRACTION94.7666
1.6-1.6440.3245110.3049900X-RAY DIFFRACTION95.1298
1.644-1.6920.35040.2859687X-RAY DIFFRACTION95.3678
1.692-1.7440.2954650.2679446X-RAY DIFFRACTION95.6106
1.744-1.8010.264840.2429139X-RAY DIFFRACTION95.7798
1.801-1.8640.2474840.2178885X-RAY DIFFRACTION96.1416
1.864-1.9350.2284800.1968588X-RAY DIFFRACTION96.3042
1.935-2.0140.214750.178267X-RAY DIFFRACTION96.6501
2.014-2.1030.2114290.1627962X-RAY DIFFRACTION97.0282
2.103-2.2060.1983930.1517691X-RAY DIFFRACTION97.0818
2.206-2.3250.2084060.1627243X-RAY DIFFRACTION97.4271
2.325-2.4660.1873790.1366883X-RAY DIFFRACTION97.542
2.466-2.6370.1833250.1316602X-RAY DIFFRACTION98.0051
2.637-2.8480.1823120.1296068X-RAY DIFFRACTION98.1086
2.848-3.1190.1813070.1355606X-RAY DIFFRACTION98.4679
3.119-3.4870.1582810.1375096X-RAY DIFFRACTION98.6606
3.487-4.0270.162580.1334514X-RAY DIFFRACTION98.8811
4.027-4.9310.1461950.1223813X-RAY DIFFRACTION99.1588
4.931-6.970.1971550.1682978X-RAY DIFFRACTION99.3027
6.97-66.7420.217780.1941666X-RAY DIFFRACTION99.2036

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