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- PDB-1eh5: CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1eh5
TitleCRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH PALMITATE
ComponentsPALMITOYL PROTEIN THIOESTERASE 1
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / GLYCOPROTEIN
Function / homology
Function and homology information


protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / sulfatide binding / pinocytosis / : / membrane raft organization / positive regulation of pinocytosis / lysosomal lumen acidification / lipid catabolic process ...protein depalmitoylation / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / sulfatide binding / pinocytosis / : / membrane raft organization / positive regulation of pinocytosis / lysosomal lumen acidification / lipid catabolic process / receptor-mediated endocytosis / brain development / 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 / negative regulation of apoptotic process / Golgi apparatus / extracellular region / nucleus / cytosol
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
PALMITIC ACID / Palmitoyl-protein thioesterase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference fourier / Resolution: 2.5 Å
AuthorsBellizzi III, J.J. / Widom, J. / Kemp, C. / Lu, J.Y. / Das, A.K. / Hofmann, S.L. / Clardy, J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis.
Authors: Bellizzi III, J.J. / Widom, J. / Kemp, C. / Lu, J.Y. / Das, A.K. / Hofmann, S.L. / Clardy, J.
#1: Journal: Nature / Year: 1995
Title: Mutations in the Palmitoyl Protein Thioesterase Gene Causing Infantile Neuronal Ceroid Lipofuscinosis
Authors: Vesa, J. / Hellsten, E. / Verkruyse, L.A. / Camp, L.A. / Rapola, J. / Santavuori, P. / Hofmann, S.L. / Peltonen, L.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Purification and Properties of a Palmitoyl Protein Thioesterase that Cleaves Palmitate from H-Ras
Authors: Camp, L.A. / Hofmann, S.L.
History
DepositionFeb 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 31, 2018Group: Database references / Experimental preparation / Category: citation_author / exptl_crystal_grow
Item: _citation_author.name / _exptl_crystal_grow.pdbx_details
Revision 1.6Feb 28, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PALMITOYL PROTEIN THIOESTERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5705
Polymers31,4471
Non-polymers1,1234
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.520, 67.520, 128.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein PALMITOYL PROTEIN THIOESTERASE 1


Mass: 31447.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Description: 10 L BIOREACTOR / Cell (production host): SF21 CELLS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P45478, palmitoyl[protein] hydrolase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAsn197, Asn212 and Asn232 are glycosylated. The OG of Ser115 is covalently modified by palmitate.

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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: 2.041 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 55% Polypropylene Glycol 400, 100 mM Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 20.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
155 %PEG4001reservoir
2100 mMBis-Tris1reservoir
312 mg/mlPPT11drop
42 mg/mlpalmitoyl-CoA1drop
520 mMHEPES1drop
6150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.0088
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 2.5→21.064 Å / Num. all: 47325 / Num. obs: 46474 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.362 / Num. unique all: 1507 / % possible all: 97.8
Reflection
*PLUS
Lowest resolution: 41.2 Å / Num. obs: 10620 / % possible obs: 97.4 % / Num. measured all: 113623

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CNSrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: difference fourier
Starting model: 1ei9 (uncomplexed ppt1)

1ei9


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 1390208.41 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Generated parameter/topology files for palmitate with XPLO2D
Details: Used simulated annealing, energy minimization, individual B-factor refinement. Used isotropic B-factor correction and bulk solvent correction.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 512 4.8 %Random
Rwork0.2262 ---
all0.2337 10900 --
obs0.2337 10620 97.4 %-
Solvent computationSolvent model: flat model / Bsol: 49.5058 Å2 / ksol: 0.34248 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 73 36 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it2.091.5
X-RAY DIFFRACTIONc_mcangle_it3.362
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it3.042.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.039
RfactorNum. reflection% reflection
Rfree0.374 92 5.3 %
Rwork0.318 1628 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramwater.top
X-RAY DIFFRACTION3water_rep.paramcarbohydrate.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.226 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.374 / % reflection Rfree: 5.3 % / Rfactor Rwork: 0.318

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