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- PDB-1ei9: CRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 -

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Basic information

Entry
Database: PDB / ID: 1ei9
TitleCRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1
ComponentsPALMITOYL PROTEIN THIOESTERASE 1
KeywordsHYDROLASE / alpha/beta hydrolase / glycoprotein
Function / homology
Function and homology information


protein depalmitoylation / palmitoyl-(protein) hydrolase activity / palmitoyl[protein] hydrolase / sulfatide binding / pinocytosis / long-chain fatty acyl-CoA hydrolase activity / membrane raft organization / positive regulation of pinocytosis / lysosomal lumen acidification / lipid catabolic process ...protein depalmitoylation / palmitoyl-(protein) hydrolase activity / palmitoyl[protein] hydrolase / sulfatide binding / pinocytosis / long-chain fatty acyl-CoA hydrolase activity / 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 / protein transport / synaptic vesicle / 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
Palmitoyl-protein thioesterase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 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: Structure / Year: 1999
Title: Producing Selenomethionine-labeled Proteins with a Baculovirus Expression Vector System
Authors: Bellizzi III, J.J. / Widom, J. / Kemp, C.W. / Clardy, J.
#2: 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.
#3: 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 24, 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 / Category: citation_author / Item: _citation_author.name
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_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_comp_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PALMITOYL PROTEIN THIOESTERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3144
Polymers31,4471
Non-polymers8673
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.350, 69.350, 128.390
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) / Cell (production host): SF21 CELLS / Production host: unidentified baculovirus / 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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 55% Polypropylene Glycol 400, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlPPT11drop
220 mMHEPES1drop
3150 mM1dropNaCl
455 %PEG4001reservoir
5100 mMBis-Tris1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONCHESS F210.9791,0.9789,0.9364
SYNCHROTRONCHESS A120.91
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 6, 1998
ADSC2CCDJul 24, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97891
30.93641
40.911
ReflectionResolution: 2.25→20.33 Å / Num. all: 15553 / Num. obs: 14962 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4 % / Rmerge(I) obs: 0.125 / % possible all: 92.4
Reflection
*PLUS
Lowest resolution: 20.9 Å / Num. obs: 14788 / % possible obs: 94.8 % / Num. measured all: 109210 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.164

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Processing

Software
NameVersionClassification
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
SCALAdata scaling
TRUNCATEdata reduction
SOLVEphasing
SHARPphasing
CNSrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high rms absF: 1081559.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: anisotropic B correction and bulk solvent correction applied. Maximum likelihood target function used. The structure was determined by MAD phasing at 3.0 Angstroms on SeMet protein expressed ...Details: anisotropic B correction and bulk solvent correction applied. Maximum likelihood target function used. The structure was determined by MAD phasing at 3.0 Angstroms on SeMet protein expressed in baculovirus/insect cells. The model was refined against a 2.25 Angstrom native data set.
RfactorNum. reflection% reflectionSelection details
Rfree0.297 714 4.9 %random
Rwork0.241 ---
all0.253 15503 --
obs0.249 14487 93.8 %-
Solvent computationSolvent model: flat model / Bsol: 75.8949 Å2 / ksol: 0.453878 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20 Å2
2---1.68 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 56 53 2319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.343
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it2.031.5
X-RAY DIFFRACTIONc_mcangle_it3.062
X-RAY DIFFRACTIONc_scbond_it2.982
X-RAY DIFFRACTIONc_scangle_it4.132.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 117 5.1 %
Rwork0.284 2195 -
obs--91.7 %
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): 2 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 41.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
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: 0.36 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.284

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