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- PDB-4x93: Crystal structure of Lysosomal Phospholipase A2 crystallized in t... -

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Basic information

Entry
Database: PDB / ID: 4x93
TitleCrystal structure of Lysosomal Phospholipase A2 crystallized in the presence of methyl arachidonyl fluorophosphonate (tetragonal 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 / phospholipase A1 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 / phospholipase A1 activity / calcium-independent phospholipase A2 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Lysosomal phospholipase A and acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_oper_list.symmetry_operation / _struct_conn.id
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
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
Revision 1.5Sep 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Nov 20, 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
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,96514
Polymers86,2422
Non-polymers2,72312
Water1,63991
1
A: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2446
Polymers43,1211
Non-polymers1,1235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7218
Polymers43,1211
Non-polymers1,6007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.820, 86.820, 365.848
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 4 - 378 / Label seq-ID: 5 - 379

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 10 molecules AB

#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.: 2 / 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.: 8 / 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 , 4 types, 95 molecules

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


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.01 Å3/Da / Density % sol: 69.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 30% PEG MME 550, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933 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: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 44707 / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.049 / Rrim(I) all: 0.165 / Χ2: 1.508 / Net I/av σ(I): 23.545 / Net I/σ(I): 4.4 / Num. measured all: 654390
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.6-2.6414.722050.7610.4280.886100
2.64-2.6914.621590.8150.380.914100
2.69-2.7414.722000.8590.3020.907100
2.74-2.814.821900.880.2720.936100
2.8-2.8614.921760.910.2270.9771000.8550.885
2.86-2.9314.821830.9330.1910.9881000.7190.744
2.93-314.922330.9580.161.0631000.6030.624
3-3.081521750.9720.1391.1361000.5220.54
3.08-3.1714.921910.9750.1071.2671000.4020.416
3.17-3.2814.921950.9810.091.3981000.3370.349
3.28-3.3914.922160.9820.0731.5191000.2740.284
3.39-3.5314.622310.9870.0651.6461000.2390.248
3.53-3.6914.522160.9890.0531.7191000.1950.202
3.69-3.8814.422310.9930.0461.8041000.1680.175
3.88-4.1213.922520.9910.0432.0161000.1540.16
4.12-4.4413.822380.9930.0412.551000.1470.153
4.44-4.8913.922790.9940.0352.6199.90.1240.129
4.89-5.5914.822890.9960.032.1141000.110.114
5.59-7.0315.423340.9970.0251.7341000.0960.1
7.03-3014.425140.9970.021.98199.60.0730.076

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Processing

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

4x90


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.517 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 2158 4.9 %RANDOM
Rwork0.1986 ---
obs0.1995 42161 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.93 Å2 / Biso mean: 62.707 Å2 / Biso min: 32.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6049 0 174 91 6314
Biso mean--87.44 47.33 -
Num. residues----753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196488
X-RAY DIFFRACTIONr_bond_other_d0.0030.026054
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9858822
X-RAY DIFFRACTIONr_angle_other_deg0.869313916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10723.493292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.608151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.21542
X-RAY DIFFRACTIONr_chiral_restr0.0860.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217179
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021507
X-RAY DIFFRACTIONr_mcbond_it1.4843.8773051
X-RAY DIFFRACTIONr_mcbond_other1.4843.8753050
X-RAY DIFFRACTIONr_mcangle_it2.5425.8123813
Refine LS restraints NCS

Ens-ID: 1 / Number: 23361 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 160 -
Rwork0.303 3054 -
all-3214 -
obs--99.84 %
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)
11.46620.4173-1.10851.2504-0.51442.11610.0438-0.0694-0.0277-0.2888-0.0274-0.0289-0.0410.172-0.01650.28370.0562-0.00780.0702-0.01890.007234.969486.604565.8475
21.41740.06270.23631.81290.47052.32360.0584-0.02240.03780.1609-0.16140.38510.0575-0.60380.1030.1884-0.0830.07110.2236-0.02140.10841.37579.122121.6907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 385
2X-RAY DIFFRACTION2B3 - 397

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