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- PDB-4x94: Crystal structure of Lysosomal Phospholipase A2 crystallized in t... -

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Basic information

Entry
Database: PDB / ID: 4x94
TitleCrystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (hexagonal form)
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: 2.7 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_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_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
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 23, 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)44,72411
Polymers43,1211
Non-polymers1,60310
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.978, 95.978, 207.943
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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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: 43121.027 Da / Num. of mol.: 1 / Fragment: UNP residues 34-412
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.23 Å3/Da / Density % sol: 61.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3
Details: 100 mM citric acid pH 3, 0.8 M ammonium sulfate ; crystallized in the presence of methyl arachidonyl fluorophosphonate

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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: 2.7→30 Å / Num. obs: 16438 / % possible obs: 94.7 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.036 / Rrim(I) all: 0.139 / Χ2: 1.552 / Net I/av σ(I): 27.816 / Net I/σ(I): 7.8 / Num. measured all: 205101
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7411.60.757650.9050.2030.781.12392.4
2.74-2.812.70.6668350.9490.1750.691.163100
2.8-2.8512.50.6488560.9390.1730.6721.189100
2.85-2.9212.50.5698470.9460.1510.591.231100
2.92-2.9812.80.4338360.9750.1140.4491.246100
2.98-3.0612.70.4028430.9760.1070.4171.259100
3.06-3.1412.70.358520.9820.0930.3631.215100
3.14-3.2312.50.2798500.9840.0750.2891.289100
3.23-3.3412.60.2368670.9880.0630.2451.328100
3.34-3.4612.70.1738460.9930.0460.1791.449100
3.46-3.612.80.158550.9960.040.1561.624100
3.6-3.7612.70.1378550.9960.0360.1421.874100
3.76-3.9612.60.1188700.9970.0310.1232.102100
3.96-4.212.60.0918720.9990.0250.0952.056100
4.2-4.5312.70.0738730.9980.020.0751.99100
4.53-4.9812.60.06289010.0170.0651.863100
4.98-5.712.40.0638940.9990.0180.0661.721100
5.7-7.1612.30.0639180.9980.0180.0661.646100
7.16-3011.10.04810140.9980.0150.0511.95699.9

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Processing

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

4x90


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 21.281 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.503 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 853 5.2 %RANDOM
Rwork0.177 15534 --
obs0.1793 15534 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.35 Å2 / Biso mean: 50.566 Å2 / Biso min: 25.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.54 Å20 Å2
2--1.09 Å20 Å2
3----3.52 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 96 34 3149
Biso mean--79.36 45.55 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193204
X-RAY DIFFRACTIONr_bond_other_d0.0030.022960
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.994371
X-RAY DIFFRACTIONr_angle_other_deg0.80636800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43623.542144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23615498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7131520
X-RAY DIFFRACTIONr_chiral_restr0.090.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02738
X-RAY DIFFRACTIONr_mcbond_it1.7523.251503
X-RAY DIFFRACTIONr_mcbond_other1.7523.2481502
X-RAY DIFFRACTIONr_mcangle_it2.9064.8741877
LS refinement shellResolution: 2.7→2.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 52 -
Rwork0.241 1096 -
all-1148 -
obs--97.45 %
Refinement TLS params.Method: refined / Origin x: 18.5141 Å / Origin y: -23.64 Å / Origin z: 11.1491 Å
111213212223313233
T0.0871 Å2-0.0724 Å2-0.0303 Å2-0.2022 Å20.0151 Å2--0.0324 Å2
L1.509 °2-0.081 °20.1537 °2-0.9345 °2-0.149 °2--1.0722 °2
S-0.032 Å °-0.1411 Å °0.0741 Å °0.0717 Å °-0.0318 Å °-0.1423 Å °-0.2601 Å °0.0607 Å °0.0638 Å °

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