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- PDB-3gro: Human palmitoyl-protein thioesterase 1 -

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Basic information

Entry
Database: PDB / ID: 3gro
TitleHuman palmitoyl-protein thioesterase 1
ComponentsPalmitoyl-protein thioesterase 1Palmitoyl(protein) hydrolase
KeywordsHYDROLASE / neuronal ceroid lipofuscinosis / neurodegeneration / Structural Genomics Consortium / SGC / Disease mutation / Disulfide bond / Glycoprotein / Lysosome / Polymorphism / Sensory transduction / Vision
Function / homology
Function and homology information


regulation of phospholipase A2 activity / protein catabolic process => GO:0030163 / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / fatty-acyl-CoA biosynthetic process / sulfatide binding / pinocytosis / : / thiolester hydrolase activity ...regulation of phospholipase A2 activity / protein catabolic process => GO:0030163 / protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / fatty-acyl-CoA biosynthetic process / sulfatide binding / pinocytosis / : / thiolester hydrolase activity / membrane raft organization / positive regulation of pinocytosis / lysophosphatidic acid binding / sphingolipid catabolic process / Fatty acyl-CoA biosynthesis / lysosomal lumen acidification / grooming behavior / neurotransmitter secretion / regulation of synapse structure or activity / response to stimulus / associative learning / neuron development / lipid catabolic process / visual perception / lysosomal lumen / adult locomotory behavior / receptor-mediated endocytosis / brain development / protein catabolic process / negative regulation of cell growth / positive regulation of receptor-mediated endocytosis / synaptic vesicle / protein transport / nervous system development / negative regulation of neuron apoptotic process / lysosome / membrane raft / axon / intracellular membrane-bounded organelle / neuronal cell body / dendrite / negative regulation of apoptotic process / Golgi apparatus / extracellular exosome / extracellular region / membrane / nucleus / cytosol
Similarity search - Function
Palmitoyl-protein thioesterase 1 / 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
Palmitoyl-protein thioesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.53 Å
AuthorsDobrovetsky, E. / Seitova, A. / Tong, Y. / Tempel, W. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Dobrovetsky, E. / Seitova, A. / Tong, Y. / Tempel, W. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Cossar, D. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human palmitoyl-protein thioesterase 1
Authors: Dobrovetsky, E. / Seitova, A. / Tong, Y. / Tempel, W. / Dong, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Cossar, D. / Park, H.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Palmitoyl-protein thioesterase 1
B: Palmitoyl-protein thioesterase 1


Theoretical massNumber of molelcules
Total (without water)68,2916
Polymers68,2912
Non-polymers04
Water43224
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-19.8 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.710, 90.642, 129.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Palmitoyl-protein thioesterase 1 / Palmitoyl(protein) hydrolase / PPT-1 / Palmitoyl-protein hydrolase 1


Mass: 34145.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPT1, PPT / Plasmid: pFHMSp-lic-C / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50897, palmitoyl[protein] hydrolase
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.4
Details: 24% PEG 3350, 0.2M Ammonium sulfate, 0.1M Sodium cacodylate. Cryoprotectant: 9 parts reservoir + 1 part 80% glycerol, pH 5.4, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 21818 / % possible obs: 100 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.17 / Χ2: 1.798 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.53-2.628.20.99321301.171100
2.62-2.738.70.77121461.20399.9
2.73-2.858.90.58321561.256100
2.85-38.90.44121491.148100
3-3.1990.32621491.197100
3.19-3.4390.20821491.183100
3.43-3.7890.14321821.532100
3.78-4.339.20.10821822.248100
4.33-5.459.10.122322.977100
5.45-508.40.08423433.87199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EI9

1ei9


Resolution: 2.53→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.177 / SU B: 9.194 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.581 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY. Programs coot, molprobity have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1233 5.695 %Thin shells
Rwork0.2 ---
obs0.202 21649 99.6 %-
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: 29.206 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---1.061 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.53→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4235 0 4 24 4263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224342
X-RAY DIFFRACTIONr_bond_other_d0.0010.022878
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.955902
X-RAY DIFFRACTIONr_angle_other_deg0.8613.0037023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03924.792192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94115693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
X-RAY DIFFRACTIONr_mcbond_it1.02222744
X-RAY DIFFRACTIONr_mcbond_other0.13121119
X-RAY DIFFRACTIONr_mcangle_it1.80134402
X-RAY DIFFRACTIONr_scbond_it1.04521598
X-RAY DIFFRACTIONr_scangle_it1.61331500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.5950.3711260.3071428157398.792
2.595-2.66600.2651518153399.022
2.666-2.7420.3031290.2441332147599.051
2.742-2.8260.2311060.2281353146999.319
2.826-2.9180.291940.2411295139799.427
2.918-3.01900.241350135899.411
3.019-3.1320.2751050.2291218132999.549
3.132-3.2580.29920.2281154125299.521
3.258-3.4020.238710.19311561227100
3.402-3.5650.261800.19510851165100
3.565-3.7550.24500.17910751125100
3.755-3.9790.224490.16710061055100
3.979-4.2490.19520.1559571009100
4.249-4.5810.156770.153867944100
4.581-5.0070.174500.153820870100
5.007-5.5780.255320.19761793100
5.578-6.4050.257460.222667713100
6.405-7.7560.183310.219588619100
7.756-10.620.157210.18482503100
10.62-300.337220.22130432799.694

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