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- PDB-2nt1: Structure of acid-beta-glucosidase at neutral pH -

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Basic information

Entry
Database: PDB / ID: 2nt1
TitleStructure of acid-beta-glucosidase at neutral pH
ComponentsGlucosylceramidase
KeywordsHYDROLASE / acid-beta-glucosidase / cerezyme / glucosylceramide / gaucher disease
Function / homology
Function and homology information


positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration ...positive regulation of protein lipidation / steryl-beta-glucosidase activity / beta-glucoside catabolic process / positive regulation of neuronal action potential / cerebellar Purkinje cell layer formation / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / galactosylceramidase / termination of signal transduction / galactosylceramidase activity / lymphocyte migration / glucosylceramidase / scavenger receptor binding / glucosylceramide catabolic process / regulation of lysosomal protein catabolic process / autophagosome organization / glucosylceramidase activity / microglial cell proliferation / sphingosine biosynthetic process / glucosyltransferase activity / regulation of TOR signaling / ceramide biosynthetic process / lipid storage / microglia differentiation / response to thyroid hormone / Glycosphingolipid catabolism / pyramidal neuron differentiation / lipid glycosylation / brain morphogenesis / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / response to pH / positive regulation of protein-containing complex disassembly / motor behavior / neuromuscular process / Transferases; Glycosyltransferases; Hexosyltransferases / hematopoietic stem cell proliferation / lysosome organization / response to testosterone / response to dexamethasone / Association of TriC/CCT with target proteins during biosynthesis / antigen processing and presentation / 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 / positive regulation of protein dephosphorylation / cell maturation / cellular response to starvation / respiratory electron transport chain / cholesterol metabolic process / lysosomal lumen / negative regulation of MAP kinase activity / determination of adult lifespan / trans-Golgi network / autophagy / negative regulation of inflammatory response / response to estrogen / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to tumor necrosis factor / T cell differentiation in thymus / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / negative regulation of neuron apoptotic 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 / 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
PHOSPHATE ION / Lysosomal acid glucosylceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLieberman, R.L. / Petsko, G.A. / Ringe, D.
CitationJournal: Nat.Chem.Biol. / Year: 2007
Title: Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease.
Authors: Lieberman, R.L. / Wustman, B.A. / Huertas, P. / Powe, A.C. / Pine, C.W. / Khanna, R. / Schlossmacher, M.G. / Ringe, D. / Petsko, G.A.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 30, 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 / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosylceramidase
B: Glucosylceramidase
C: Glucosylceramidase
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,85386
Polymers222,5614
Non-polymers8,29382
Water24,2121344
1
A: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,85623
Polymers55,6401
Non-polymers2,21622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,57120
Polymers55,6401
Non-polymers1,93119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,04625
Polymers55,6401
Non-polymers2,40624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: Glucosylceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,38118
Polymers55,6401
Non-polymers1,74117
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21170 Å2
ΔGint-435 kcal/mol
Surface area69610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.185, 91.792, 153.036
Angle α, β, γ (deg.)90.000, 110.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 1 - 497 / Label seq-ID: 1 - 497

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
12BB
22DD

NCS ensembles :
ID
1
2

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Components

#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: 55640.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBA / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04062, glucosylceramidase
#2: 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.: 4
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
#3: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 78 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1344 / Source method: isolated from a natural source / Formula: H2O

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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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M Na dihydrogen phosphate 0.8 M K dihydrogen phosphate 0.1 M Hepes buffer pH 7.5 Cryoprotected in 2 M Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 119558 / % possible obs: 95.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.1 Å2 / Rsym value: 0.106 / Χ2: 1.432 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.4 / Num. unique all: 9993 / Χ2: 1.114 / % possible all: 79.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NT0

2nt0


Resolution: 2.3→19.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.679 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6021 5 %RANDOM
Rwork0.175 ---
obs0.178 119536 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.096 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.06 Å2
2---0.09 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15720 0 446 1344 17510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02216584
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.97122668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1851984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50923.444720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.744152516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3861584
X-RAY DIFFRACTIONr_chiral_restr0.1350.22412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212532
X-RAY DIFFRACTIONr_nbd_refined0.2230.28004
X-RAY DIFFRACTIONr_nbtor_refined0.3110.210701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.21340
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.222
X-RAY DIFFRACTIONr_mcbond_it1.0951.510226
X-RAY DIFFRACTIONr_mcangle_it1.798216072
X-RAY DIFFRACTIONr_scbond_it2.76637349
X-RAY DIFFRACTIONr_scangle_it4.0834.56596
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1988MEDIUM POSITIONAL0.110.5
1A1942LOOSE POSITIONAL0.35
1A1988MEDIUM THERMAL0.632
1A1942LOOSE THERMAL1.2810
2B1988MEDIUM POSITIONAL0.110.5
2B1942LOOSE POSITIONAL0.45
2B1988MEDIUM THERMAL0.552
2B1942LOOSE THERMAL1.2810
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 362 -
Rwork0.254 6627 -
obs-6989 76.46 %

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