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- PDB-3u0v: Crystal Structure Analysis of human LYPLAL1 -

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Basic information

Entry
Database: PDB / ID: 3u0v
TitleCrystal Structure Analysis of human LYPLAL1
ComponentsLysophospholipase-like protein 1
KeywordsHYDROLASE / alpha / beta hydrolase fold
Function / homology
Function and homology information


negative regulation of Golgi to plasma membrane protein transport / palmitoyl[protein] hydrolase / palmitoyl-(protein) hydrolase activity / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / phosphatidylcholine lysophospholipase activity / negative regulation of cGAS/STING signaling pathway / mitochondrion / 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
Lysophospholipase-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsBurger, M. / Zimmermann, T.J. / Kondoh, Y. / Stege, P. / Watanabe, N. / Osada, H. / Waldmann, H. / Vetter, I.R.
CitationJournal: J.Lipid Res. / Year: 2012
Title: Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases
Authors: Burger, M. / Zimmermann, T.J. / Kondoh, Y. / Stege, P. / Watanabe, N. / Osada, H. / Waldmann, H. / Vetter, I.R.
History
DepositionSep 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysophospholipase-like protein 1


Theoretical massNumber of molelcules
Total (without water)26,5221
Polymers26,5221
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.782, 60.778, 76.620
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 Lysophospholipase-like protein 1


Mass: 26521.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LYPLAL1 / Plasmid: pGEX 4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon +RIL
References: UniProt: Q5VWZ2, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REF 1 AND 3 OF DATABASE UNIPROTKB/SWISSPROT Q5VWZ2 (LYPL1_HUMAN). I131M IS ...THE SEQUENCE IS BASED ON REF 1 AND 3 OF DATABASE UNIPROTKB/SWISSPROT Q5VWZ2 (LYPL1_HUMAN). I131M IS NATURAL VARIANT.

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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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% w/v PEG 3350, 0.1M Bis-Tris pH 5.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2010
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.72→33.73 Å / Num. obs: 23960 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.419 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.72-1.760.4680.3463.15180175616560.41394.3
1.76-1.810.370.294.116402173017070.33798.7
1.81-1.870.2710.2565.648144168116720.28799.5
1.87-1.920.2220.2027.268585164216380.22499.8
1.92-1.990.1770.1818.38179158315800.20199.8
1.99-2.060.1510.14510.167735153115280.16299.8
2.06-2.130.1270.12111.747229148514710.13699.1
2.13-2.220.1010.10614.087536143614340.11899.9
2.22-2.320.0820.09316.057135137513710.10499.7
2.32-2.430.0710.08118.096752131713110.09199.5
2.43-2.560.0740.07918.796115125412420.08999
2.56-2.720.0620.07221.346084119411820.08199
2.72-2.910.0530.05725.255844112711130.06398.8
2.91-3.140.0440.04829.645227103710220.05398.6
3.14-3.440.0350.0433.9246729839550.04697.2
3.44-3.850.0260.03241.6144838828620.03697.7
3.85-4.440.020.02745.4838067917610.03196.2
4.44-5.440.0190.02645.2931086896510.02994.5
5.44-7.690.0230.0341.1425455375110.03495.2
7.690.0190.02649.9913153222930.02991

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0093refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1fj2

1fj2


Resolution: 1.72→33.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1909 / WRfactor Rwork: 0.1582 / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8823 / SU B: 1.941 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1099 / SU Rfree: 0.1088 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 1216 5.1 %RANDOM
Rwork0.1735 ---
obs0.1753 23958 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.48 Å2 / Biso mean: 19.6591 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.72→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 0 144 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0221850
X-RAY DIFFRACTIONr_angle_refined_deg2.5781.9472520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.83724.30479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46715331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.272157
X-RAY DIFFRACTIONr_chiral_restr0.2370.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211381
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 95 -
Rwork0.262 1448 -
all-1543 -
obs--93.91 %

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