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- PDB-1pja: The crystal structure of palmitoyl protein thioesterase-2 reveals... -

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Basic information

Entry
Database: PDB / ID: 1pja
TitleThe crystal structure of palmitoyl protein thioesterase-2 reveals the basis for divergent substrate specificities of the two lysosomal thioesterases (PPT1 and PPT2)
ComponentsPalmitoyl-protein thioesterase 2 precursor
KeywordsHYDROLASE / glycoprotein / lysosome
Function / homology
Function and homology information


palmitoyl hydrolase activity / palmitoyl-(protein) hydrolase activity / thiolester hydrolase activity / palmitoyl-CoA hydrolase / fatty-acyl-CoA biosynthetic process / fatty acyl-CoA hydrolase activity / Fatty acyl-CoA biosynthesis / lysosomal lumen / lysosome / intracellular membrane-bounded organelle ...palmitoyl hydrolase activity / palmitoyl-(protein) hydrolase activity / thiolester hydrolase activity / palmitoyl-CoA hydrolase / fatty-acyl-CoA biosynthetic process / fatty acyl-CoA hydrolase activity / Fatty acyl-CoA biosynthesis / lysosomal lumen / lysosome / intracellular membrane-bounded organelle / extracellular exosome / extracellular region
Similarity search - Function
Palmitoyl protein thioesterase / Palmitoyl protein thioesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysosomal thioesterase PPT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCalero, G. / Gupta, P. / Nonato, M.C. / Tandel, S. / Biehl, E.R. / Hofmann, S.L. / Clardy, J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2.
Authors: Calero, G. / Gupta, P. / Nonato, M.C. / Tandel, S. / Biehl, E.R. / Hofmann, S.L. / Clardy, J.
History
DepositionJun 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoyl-protein thioesterase 2 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8405
Polymers34,3421
Non-polymers4974
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.520, 148.520, 152.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Palmitoyl-protein thioesterase 2 precursor / Palmitoyl- protein hydrolase 2 / PPT-2 / G14


Mass: 34342.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPT2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UMR5, palmitoyl[protein] hydrolase
#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.: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8-2.2M ammonium sulfate, 8% methyl-pentane-diol, 100 mM MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / PH range low: 6.5 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
3100 mMsodium cacodylate1reservoirpH5.5-6.5
48 %MPD1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 34721 / Num. obs: 34721 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.046 / Net I/σ(I): 15.7
Reflection shellHighest resolution: 2.7 Å / Mean I/σ(I) obs: 2.5
Reflection
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40 Å / σ(F): 0
RfactorNum. reflection
Rfree0.242 -
Rwork0.221 -
all0.251 27511
obs0.251 27511
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 32 50 2243
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.09
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.3

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