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- PDB-4x97: Crystal structure of Lysosomal Phospholipase A2 in complex with m... -

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Basic information

Entry
Database: PDB / ID: 4x97
TitleCrystal structure of Lysosomal Phospholipase A2 in complex with methyl arachidonyl fluorophosphonate (MAFP)
ComponentsGroup XV phospholipase A2
KeywordsTRANSFERASE / hydrolase / phospholipase / MAFP / 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
METHYL ARACHIDONYL FLUOROPHOSPHONATE / PHOSPHATE ION / Lysosomal phospholipase A and acyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 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 1.3Nov 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_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
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 / 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

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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)178,87433
Polymers172,4844
Non-polymers6,39029
Water4,179232
1
A: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7108
Polymers43,1211
Non-polymers1,5897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7459
Polymers43,1211
Non-polymers1,6248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7108
Polymers43,1211
Non-polymers1,5897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Group XV phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7108
Polymers43,1211
Non-polymers1,5897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.147, 85.495, 88.852
Angle α, β, γ (deg.)88.850, 70.870, 79.740
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:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPROAA3 - 3794 - 380
21ARGARGPROPROBB3 - 3794 - 380
12HISHISGLYGLYAA4 - 3785 - 379
22HISHISGLYGLYCC4 - 3785 - 379
13HISHISGLYGLYAA4 - 3785 - 379
23HISHISGLYGLYDD4 - 3785 - 379
14HISHISGLYGLYBB4 - 3785 - 379
24HISHISGLYGLYCC4 - 3785 - 379
15HISHISGLYGLYBB4 - 3785 - 379
25HISHISGLYGLYDD4 - 3785 - 379
16HISHISPROPROCC4 - 3795 - 380
26HISHISPROPRODD4 - 3795 - 380

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
Details: LPLA2 is covalently linked to MAFP via S165 / 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.: 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, 245 molecules

#3: Chemical
ChemComp-MAY / METHYL ARACHIDONYL FLUOROPHOSPHONATE / MAFP


Mass: 370.482 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36FO2P / Comment: inhibitor*YM
#4: 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
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
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: 21-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 52162 / % possible obs: 93.2 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.089 / Rrim(I) all: 0.125 / Χ2: 0.844 / Net I/av σ(I): 8.514 / Net I/σ(I): 6.4 / Num. measured all: 101664
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.71.20.5731110.2220.5730.811.2294
2.7-2.741.80.425050.6860.40.5660.60289.1
2.74-2.81.90.40627280.6480.4060.5740.65797.6
2.8-2.851.90.33627740.7660.3360.4760.62998.1
2.85-2.9220.30327420.7860.3030.4280.64198.1
2.92-2.9820.26227310.8280.2620.370.64598.3
2.98-3.0620.23127520.8510.2310.3270.71798.3
3.06-3.1420.19527990.8950.1950.2760.75898.4
3.14-3.2320.16327110.9280.1630.230.7898.5
3.23-3.3420.13527680.9490.1350.1910.78998.5
3.34-3.4620.11227620.960.1120.1590.90198.6
3.46-3.620.09627350.9710.0960.1360.92898.6
3.6-3.7620.08327580.9770.0830.1180.98298.4
3.76-3.9620.07327620.980.0730.1031.01598.6
3.96-4.220.05527420.9890.0550.0780.97598.7
4.2-4.5320.04327750.9930.0430.0610.95798.6
4.53-4.9820.04127910.9930.0410.0580.93998.9
4.98-5.720.04627540.9910.0460.0650.9499
5.7-7.1620.04827660.9910.0480.0680.95698.9
7.16-301.90.03626960.9930.0360.0511.18496.4

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Phasing

PhasingMethod: molecular replacement

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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: 2.65→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.048 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 2558 4.9 %RANDOM
Rwork0.1794 49603 --
obs0.1813 49603 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.69 Å2 / Biso mean: 39.398 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å21.46 Å2-0.29 Å2
2---1 Å2-0.7 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12098 0 372 232 12702
Biso mean--54.04 24.9 -
Num. residues----1506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912917
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212020
X-RAY DIFFRACTIONr_angle_refined_deg1.7881.98917610
X-RAY DIFFRACTIONr_angle_other_deg1.262327623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1651524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42723.494581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.054152018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9941582
X-RAY DIFFRACTIONr_chiral_restr0.0970.21901
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114344
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023008
X-RAY DIFFRACTIONr_mcbond_it2.0182.2386051
X-RAY DIFFRACTIONr_mcbond_other2.0142.2376050
X-RAY DIFFRACTIONr_mcangle_it3.2823.3527566
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A243680.06
12B243680.06
21A241810.06
22C241810.06
31A241330.07
32D241330.07
41B243200.06
42C243200.06
51B244240.05
52D244240.05
61C242220.06
62D242220.06
LS refinement shellResolution: 2.65→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 109 -
Rwork0.259 1905 -
all-2014 -
obs--49.45 %
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)
10.5954-0.3895-0.19011.80020.521.02490.0992-0.0019-0.07450.0409-0.0741-0.00840.1808-0.0187-0.02510.1050.0283-0.07080.0888-0.01560.07257.4835-18.0773-16.5478
21.0194-0.32580.46441.0593-0.14870.95410.07470.0321-0.0015-0.1371-0.09130.024-0.06640.02770.01660.04710.0459-0.01540.0951-0.02650.008-20.873621.5879-20.8039
30.5529-0.2188-0.02071.30340.78911.8902-0.0853-0.02560.03810.34780.0639-0.08640.17920.030.02140.1840.0406-0.06090.0878-0.02070.0247-4.070517.006918.537
40.9455-1.06090.95552.3347-1.9263.4184-0.0985-0.1003-0.1550.37880.39920.2629-0.1391-0.4497-0.30070.15780.0226-0.00490.13260.05110.068323.4482-24.107423.5394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 405
2X-RAY DIFFRACTION2B3 - 405
3X-RAY DIFFRACTION3C4 - 405
4X-RAY DIFFRACTION4D4 - 405

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