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

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Basic information

Entry
Database: PDB / ID: 1exw
TitleCRYSTAL STRUCTURE OF PALMITOYL PROTEIN THIOESTERASE 1 COMPLEXED WITH HEXADECYLSULFONYL FLUORIDE
ComponentsPALMITOYL PROTEIN THIOESTERASE 1
KeywordsHYDROLASE / alpha/beta hydrolase / palmitoyl protein thioesterase / PMSF
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / 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 ...long-chain fatty acyl-CoA hydrolase activity / 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 / 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
1-HEXADECANOSULFONIC ACID / Palmitoyl-protein thioesterase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsBellizzi III, J.J. / Clardy, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Structural basis for the insensitivity of a serine enzyme (palmitoyl-protein thioesterase) to phenylmethylsulfonyl fluoride.
Authors: Das, A.K. / Bellizzi III, J.J. / Tandel, S. / Biehl, E. / Clardy, J. / Hofmann, S.L.
History
DepositionMay 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 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 / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.details / _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

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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)32,6205
Polymers31,4471
Non-polymers1,1734
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.060, 69.060, 128.030
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: Chemical ChemComp-HDS / 1-HEXADECANOSULFONIC ACID


Mass: 306.504 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 55% PPG 400, 0.1 M Bis Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
220 mMHEPES1drop
3150 mM1dropNaCl
40.01 %Triton X-1001drop
51 mMHDSF1drop
655 %PEG4001reservoir
7100 mMbis-Tris 1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→36.27 Å / Num. all: 79642 / Num. obs: 79642 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.216 / Num. unique all: 15447 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CNSrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementResolution: 2.4→19.71 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2044459.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: GENERATED PARAMETER/TOPOLOGY FILES FOR HDSF 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
Rfree0.288 630 5 %RANDOM
Rwork0.243 ---
obs0.243 12638 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.33 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 53.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.13 Å20 Å20 Å2
2--7.13 Å20 Å2
3----14.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 75 40 2325
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0121.5
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_torsion_deg252
X-RAY DIFFRACTIONc_torsion_impr_deg1.412.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.379 100 4.9 %
Rwork0.325 1961 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAMWATER.TOP
X-RAY DIFFRACTION3PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4HDS.PARHDS.TOP

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