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- PDB-4x92: Crystal structure of Lysosomal Phospholipase A2-S165A -

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Basic information

Entry
Database: PDB / ID: 4x92
TitleCrystal structure of Lysosomal Phospholipase A2-S165A
ComponentsGroup XV phospholipase A2
KeywordsTRANSFERASE / hydrolase / phospholipase / esterase / acyltransferase
Function / homology
Function and homology information


acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / phosphatidylserine metabolic process / Hydrolysis of LPC / diacylglycerol biosynthetic process / lysophospholipase / glycerophospholipid metabolic process / O-acyltransferase activity / phospholipase A1 / calcium-independent phospholipase A2 activity ...acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / phosphatidylserine metabolic process / Hydrolysis of LPC / diacylglycerol biosynthetic process / lysophospholipase / glycerophospholipid metabolic process / O-acyltransferase activity / phospholipase A1 / calcium-independent phospholipase A2 activity / phospholipase A1 activity / ceramide metabolic process / phosphatidylglycerol metabolic process / fatty acid catabolic process / phosphatidylcholine metabolic process / phospholipase A2 / phosphatidylcholine catabolic process / phosphatidylcholine lysophospholipase activity / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / lysosome / intracellular membrane-bounded organelle / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / membrane
Similarity search - Function
Lecithin:cholesterol/phospholipid:diacylglycerol acyltransferase / Lecithin:cholesterol acyltransferase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysosomal phospholipase A and acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGlukhova, A. / Tesmer, J.J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086865 United States
CitationJournal: Nat Commun / Year: 2015
Title: Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase.
Authors: Glukhova, A. / Hinkovska-Galcheva, V. / Kelly, R. / Abe, A. / Shayman, J.A. / Tesmer, J.J.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 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
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9905
Polymers43,1051
Non-polymers8854
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint12 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.239, 257.239, 257.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Group XV phospholipase A2 / 1-O-acylceramide synthase / ACS / LCAT-like lysophospholipase / LLPL / Lysophospholipase 3 / ...1-O-acylceramide synthase / ACS / LCAT-like lysophospholipase / LLPL / Lysophospholipase 3 / Lysosomal phospholipase A2 / LPLA2


Mass: 43105.027 Da / Num. of mol.: 1 / Fragment: UNP residues 34-412 / Mutation: S165A
Source method: isolated from a genetically manipulated source
Details: S165A mutant of human Lysosomal Phospholipase A2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G15, LYPLA3, UNQ341/PRO540 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NCC3, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Na cacodylate pH 6.5, 10% PEG 8000, 200 mM Mg(CH3COO) in the presence of DOPC liposomes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97937 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 14922 / % possible obs: 98.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.098 / Rrim(I) all: 0.23 / Χ2: 1.115 / Net I/av σ(I): 8.938 / Net I/σ(I): 3.9 / Num. measured all: 83833
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3-3.055.60.937220.6050.4280.887100
3.05-3.115.60.8247530.7130.3770.881000.91
3.11-3.175.60.7267270.7550.3310.90499.90.801
3.17-3.235.60.6097330.8210.2770.871000.672
3.23-3.35.60.5267470.8640.2380.9411000.58
3.3-3.385.70.4717370.8580.2130.9771000.519
3.38-3.465.70.3677290.9010.1661.02699.90.404
3.46-3.565.70.3257320.9260.1481.01699.90.358
3.56-3.665.70.2937470.9480.1321.03399.50.322
3.66-3.785.60.2527430.9630.1141.06799.60.278
3.78-3.915.70.2147390.9730.0961.11199.50.236
3.91-4.075.70.1787520.9810.081.08299.30.196
4.07-4.255.60.1547430.9830.0691.12299.10.169
4.25-4.485.70.1417430.9870.0641.2398.90.155
4.48-4.765.60.1427420.9890.0651.51898.30.157
4.76-5.125.70.1447460.9820.0651.41797.80.159
5.12-5.645.60.1457600.9870.0651.22597.60.159
5.64-6.445.60.1447510.9840.0651.09496.90.158
6.44-8.095.60.1077650.9890.0491.11895.40.118
8.09-305.20.0788110.9930.0361.78593.10.086

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X90

4x90


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 26.723 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.78 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 764 5.1 %RANDOM
Rwork0.1883 14138 --
obs0.19 14138 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.48 Å2 / Biso mean: 43.389 Å2 / Biso min: 3.99 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 56 20 3105
Biso mean--60.34 22.61 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193183
X-RAY DIFFRACTIONr_bond_other_d0.0010.022961
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9784341
X-RAY DIFFRACTIONr_angle_other_deg0.77536798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0035378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80923.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7815501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7051521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
X-RAY DIFFRACTIONr_mcbond_it1.2253.2191509
X-RAY DIFFRACTIONr_mcbond_other1.2193.2171508
X-RAY DIFFRACTIONr_mcangle_it2.0944.8261885
LS refinement shellResolution: 3.002→3.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 61 -
Rwork0.291 1025 -
all-1086 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: -26.8048 Å / Origin y: 60.1309 Å / Origin z: 37.3837 Å
111213212223313233
T0.025 Å2-0.0223 Å2-0.0111 Å2-0.0271 Å20.0096 Å2--0.0067 Å2
L1.0253 °20.2563 °20.0419 °2-1.0355 °20.2897 °2--2.1908 °2
S-0.0119 Å °0.0313 Å °0.0176 Å °-0.0239 Å °0.0297 Å °-0.025 Å °0.0007 Å °0.121 Å °-0.0178 Å °

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