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- PDB-4x90: Crystal structure of Lysosomal Phospholipase A2 -

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Basic information

Entry
Database: PDB / ID: 4x90
TitleCrystal structure of Lysosomal Phospholipase A2
ComponentsGroup XV phospholipase A2
KeywordsTRANSFERASE / hydrolase / phospholipase / esterase / acyltransferase
Function / homology
Function and homology information


acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity ...acylglycerol O-acyltransferase activity / phosphatidylethanolamine catabolic process / Hydrolysis of LPC / phosphatidylserine metabolic process / phosphatidyl phospholipase B activity / lysophospholipase / glycerophospholipid metabolic process / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / calcium-independent phospholipase A2 activity / diacylglycerol biosynthetic process / phosphatidylglycerol metabolic process / ceramide metabolic process / phosphatidylcholine catabolic process / fatty acid catabolic process / phosphatidylcholine metabolic process / lysophospholipase activity / phospholipase A2 / phospholipid metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phospholipid binding / lysosome / intracellular membrane-bounded organelle / extracellular space / zinc ion binding / extracellular exosome / extracellular region / 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
PHOSPHATE ION / Lysosomal phospholipase A and acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_close_contact / struct_conn
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 / _struct_conn.id
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group XV phospholipase A2
B: Group XV phospholipase A2
C: Group XV phospholipase A2
D: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,15346
Polymers172,4844
Non-polymers6,66942
Water19,1861065
1
A: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,96513
Polymers43,1211
Non-polymers1,84412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,61110
Polymers43,1211
Non-polymers1,4909
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,61110
Polymers43,1211
Non-polymers1,4909
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,96513
Polymers43,1211
Non-polymers1,84412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.806, 91.151, 100.266
Angle α, β, γ (deg.)78.130, 88.460, 88.500
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 379
2010B4 - 379
1020A4 - 379
2020C4 - 379
1030A4 - 379
2030D4 - 379
1040B4 - 379
2040C4 - 379
1050B4 - 379
2050D4 - 379
1060C4 - 379
2060D4 - 379

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein / Sugars , 2 types, 20 molecules ABCD

#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.: 4 / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16 / 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

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Non-polymers , 5 types, 1091 molecules

#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 3.28 Å3/Da / Density % sol: 62.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 3.5% PEG 8000, 28% MPD, 300 mM (NH4)2HPO4

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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: 1.83→30 Å / Num. obs: 183439 / % possible obs: 97.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.095 / Χ2: 1.191 / Net I/av σ(I): 17.917 / Net I/σ(I): 6.7 / Num. measured all: 726111
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.83-1.863.90.63189660.68696.4
1.86-1.93.90.56490800.72696.5
1.9-1.933.90.47290830.77296.6
1.93-1.973.90.4190690.77796.8
1.97-2.013.90.34791280.7997
2.01-2.063.90.30590620.87397.1
2.06-2.1140.26691470.90297.2
2.11-2.1740.23890660.90397.3
2.17-2.2340.21291730.9697.6
2.23-2.3140.18991870.99997.7
2.31-2.3940.16591781.01297.8
2.39-2.4840.14891871.05798
2.48-2.640.13292131.09198.2
2.6-2.7340.11392041.18798.3
2.73-2.940.192331.23798.5
2.9-3.1340.08292571.3898.6
3.13-3.4440.06792901.61798.8
3.44-3.9440.05892701.90699.1
3.94-4.963.90.05393022.31399.2
4.96-303.90.05893442.53699.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.506 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1733 9229 5 %RANDOM
Rwork0.1541 174210 --
obs0.155 174210 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.35 Å2 / Biso mean: 26.422 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å2-0.24 Å20.13 Å2
2---0.22 Å20.2 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12076 0 476 1065 13617
Biso mean--42.16 36.8 -
Num. residues----1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913498
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212557
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.99118501
X-RAY DIFFRACTIONr_angle_other_deg1.168328856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165.0061624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36423.563609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.529152088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2451584
X-RAY DIFFRACTIONr_chiral_restr0.0850.22015
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115191
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023170
X-RAY DIFFRACTIONr_mcbond_it1.2711.776274
X-RAY DIFFRACTIONr_mcbond_other1.2711.7696273
X-RAY DIFFRACTIONr_mcangle_it2.042.6447893
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A235120.09
12B235120.09
21A235670.09
22C235670.09
31A242480.06
32D242480.06
41B242200.06
42C242200.06
51B235490.09
52D235490.09
61C234670.09
62D234670.09
LS refinement shellResolution: 1.838→1.886 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 586 -
Rwork0.217 11158 -
all-11744 -
obs--83.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1993-0.1050.04190.3876-0.33661.12020.0041-0.0017-0.0216-0.01160.01040.00660.0946-0.0071-0.01460.011-0.00470.00360.0144-0.00780.03151.0334-14.498221.4187
20.1432-0.0543-0.06451.18370.66911.10730.02030.0322-0.017-0.0625-0.02440.0079-0.1103-0.08350.0040.01560.00840.00220.0162-0.00290.0260.309329.509625.8511
30.22880.12530.080.9620.49870.81930.0115-0.02280.00790.0304-0.018-0.00660.0515-0.0450.00650.00850.0092-0.00040.0362-0.0010.05-2.3867-29.2064-25.7174
40.16240.0941-0.05410.7004-0.39371.08350.0081-0.00320.01570.02140.0108-0.0132-0.0919-0.0094-0.0190.0087-0.0007-0.00150.0227-0.0040.04560.880514.8439-21.3974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 404
2X-RAY DIFFRACTION2B4 - 403
3X-RAY DIFFRACTION3C4 - 403
4X-RAY DIFFRACTION4D4 - 404

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