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- PDB-6qgs: Crystal structure of APT1 bound to palmitic acid. -

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Basic information

Entry
Database: PDB / ID: 6qgs
TitleCrystal structure of APT1 bound to palmitic acid.
ComponentsAcyl-protein thioesterase 1
KeywordsHYDROLASE / acyl-protein thioesterase / palmitic acid / Depalmitoylation
Function / homology
Function and homology information


protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity ...protein depalmitoylation / negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / negative regulation of aggrephagy / phospholipase activity / lipase activity / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / phosphatidylcholine lysophospholipase activity / fatty acid transport / eNOS activation / fatty acid metabolic process / RAS processing / nuclear membrane / endoplasmic reticulum / mitochondrion / extracellular exosome / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / Acyl-protein thioesterase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.755 Å
AuthorsAudagnotto, M. / Marcaida, M.J. / Ho, S. / Pojer, F. / Van der Goot, G. / Dal Peraro, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_157153 Switzerland
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains.
Authors: Abrami, L. / Audagnotto, M. / Ho, S. / Marcaida, M.J. / Mesquita, F.S. / Anwar, M.U. / Sandoz, P.A. / Fonti, G. / Pojer, F. / Dal Peraro, M. / van der Goot, F.G.
History
DepositionJan 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Acyl-protein thioesterase 1
D: Acyl-protein thioesterase 1
A: Acyl-protein thioesterase 1
C: Acyl-protein thioesterase 1
E: Acyl-protein thioesterase 1
F: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,5129
Polymers149,9636
Non-polymers5483
Water3,531196
1
B: Acyl-protein thioesterase 1


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2502
Polymers24,9941
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Acyl-protein thioesterase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2863
Polymers24,9941
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Acyl-protein thioesterase 1


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Acyl-protein thioesterase 1


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Acyl-protein thioesterase 1


Theoretical massNumber of molelcules
Total (without water)24,9941
Polymers24,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.660, 81.660, 441.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Acyl-protein thioesterase 1 / hAPT1 / Lysophospholipase 1 / Lysophospholipase I / LysoPLA I


Mass: 24993.869 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLA1, APT1, LPL1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75608, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% of polyethylene glycol (PEG) 8000, 0.2 M potassium bromide, 01.M sodium acetate at pH 5.5,10%w/v PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 2.755→49.95 Å / Num. obs: 73690 / % possible obs: 99.7 % / Redundancy: 14 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 20
Reflection shellResolution: 2.755→2.92 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260?)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FJ2

1fj2


Resolution: 2.755→49.948 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.86
RfactorNum. reflection% reflection
Rfree0.2301 3664 4.98 %
Rwork0.1837 --
obs0.186 73550 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.755→49.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10007 0 37 196 10240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310275
X-RAY DIFFRACTIONf_angle_d0.54913958
X-RAY DIFFRACTIONf_dihedral_angle_d5.0456221
X-RAY DIFFRACTIONf_chiral_restr0.0431595
X-RAY DIFFRACTIONf_plane_restr0.0041802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7552-2.79140.37621270.31542466X-RAY DIFFRACTION92
2.7914-2.82970.33361440.25282749X-RAY DIFFRACTION100
2.8297-2.87010.27791380.22762626X-RAY DIFFRACTION100
2.8701-2.91290.24521450.20452745X-RAY DIFFRACTION100
2.9129-2.95840.27031430.20952681X-RAY DIFFRACTION100
2.9584-3.00690.27331460.20282712X-RAY DIFFRACTION100
3.0069-3.05880.29081370.21752660X-RAY DIFFRACTION100
3.0588-3.11440.27181460.20932723X-RAY DIFFRACTION100
3.1144-3.17430.24271420.21282671X-RAY DIFFRACTION100
3.1743-3.23910.30861410.20272714X-RAY DIFFRACTION100
3.2391-3.30950.28411430.21252684X-RAY DIFFRACTION100
3.3095-3.38640.25061360.20382740X-RAY DIFFRACTION100
3.3864-3.47110.23761340.20682643X-RAY DIFFRACTION100
3.4711-3.56490.30771420.18422732X-RAY DIFFRACTION100
3.5649-3.66980.21941370.17622688X-RAY DIFFRACTION100
3.6698-3.78820.23711430.17212677X-RAY DIFFRACTION100
3.7882-3.92360.2271450.17842713X-RAY DIFFRACTION100
3.9236-4.08060.21091430.1652714X-RAY DIFFRACTION100
4.0806-4.26620.22371450.15822700X-RAY DIFFRACTION100
4.2662-4.4910.15981430.14332683X-RAY DIFFRACTION100
4.491-4.77220.20711390.15052705X-RAY DIFFRACTION100
4.7722-5.14030.16961440.15742671X-RAY DIFFRACTION100
5.1403-5.65690.2171360.1742690X-RAY DIFFRACTION100
5.6569-6.4740.18871380.17662714X-RAY DIFFRACTION100
6.474-8.15080.2041490.17732705X-RAY DIFFRACTION100
8.1508-49.95590.17941380.17012680X-RAY DIFFRACTION100

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