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- PDB-6aun: calcium-independent phospholipase A2 beta -

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Basic information

Entry
Database: PDB / ID: 6aun
Titlecalcium-independent phospholipase A2 beta
ComponentsPLA2G6, iPLA2beta
KeywordsHYDROLASE / phospholipase / iPLA2beta / calcium-independent / PLA2G6 / PNPLA9 / calmodulin binding / ATP binding
Function / homology
Function and homology information


phosphatidylethanolamine catabolic process / : / phosphatidyl phospholipase B activity / lysophospholipase / : / phosphatidic acid metabolic process / palmitoyl-CoA hydrolase / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / calcium-independent phospholipase A2 activity ...phosphatidylethanolamine catabolic process / : / phosphatidyl phospholipase B activity / lysophospholipase / : / phosphatidic acid metabolic process / palmitoyl-CoA hydrolase / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / calcium-independent phospholipase A2 activity / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / lysophospholipase activity / serine hydrolase activity / phospholipase A2 / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / membrane => GO:0016020 / mitochondrion / plasma membrane
Similarity search - Function
Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Domain of unknown function DUF3447 / Ankyrin repeat / Acyl transferase/acyl hydrolase/lysophospholipase / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats ...Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Domain of unknown function DUF3447 / Ankyrin repeat / Acyl transferase/acyl hydrolase/lysophospholipase / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
85/88 kDa calcium-independent phospholipase A2
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.951 Å
AuthorsMalley, K. / Koroleva, O. / Miller, I. / Sanishvili, R. / Jenkins, C.M. / Gross, R.W. / Korolev, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS094854 United States
American Heart Association0665513Z United States
CASISCASIS-2012-1 United States
CitationJournal: Nat Commun / Year: 2018
Title: The structure of iPLA2beta reveals dimeric active sites and suggests mechanisms of regulation and localization.
Authors: Malley, K.R. / Koroleva, O. / Miller, I. / Sanishvili, R. / Jenkins, C.M. / Gross, R.W. / Korolev, S.
History
DepositionSep 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLA2G6, iPLA2beta
B: PLA2G6, iPLA2beta


Theoretical massNumber of molelcules
Total (without water)167,9302
Polymers167,9302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, sedimentation velocity, cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-32 kcal/mol
Surface area56910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)266.061, 266.061, 79.375
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein PLA2G6, iPLA2beta


Mass: 83965.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A3L7I2I8*PLUS, phospholipase A2

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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: 4.83 Å3/Da / Density % sol: 74 % / Description: rods
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 10% PEG3350, 0.2 M sodium/potassium salt
PH range: 5.0-7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2015
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.95→39.95 Å / Num. obs: 24660 / % possible obs: 86.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.7 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.044 / Net I/σ(I): 17
Reflection shellResolution: 3.95→4.09 Å / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 906 / CC1/2: 0.7 / Rpim(I) all: 0.46 / % possible all: 32

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.951→39.112 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3097 2461 9.98 %Random
Rwork0.2565 ---
obs0.2618 24647 86.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.951→39.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 0 0 9396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059564
X-RAY DIFFRACTIONf_angle_d1.06112930
X-RAY DIFFRACTIONf_dihedral_angle_d3.8245828
X-RAY DIFFRACTIONf_chiral_restr0.0521458
X-RAY DIFFRACTIONf_plane_restr0.0081690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9506-4.02650.3738420.2514389X-RAY DIFFRACTION27
4.0265-4.10860.209470.2514559X-RAY DIFFRACTION39
4.1086-4.19790.2969800.2724686X-RAY DIFFRACTION48
4.1979-4.29540.32321030.2592859X-RAY DIFFRACTION62
4.2954-4.40270.31011400.25951211X-RAY DIFFRACTION86
4.4027-4.52160.331350.26611312X-RAY DIFFRACTION94
4.5216-4.65440.30131460.25051410X-RAY DIFFRACTION98
4.6544-4.80440.3311540.25191394X-RAY DIFFRACTION100
4.8044-4.97580.30671680.26441431X-RAY DIFFRACTION100
4.9758-5.17460.38971550.26811420X-RAY DIFFRACTION100
5.1746-5.40950.31191660.26061406X-RAY DIFFRACTION100
5.4095-5.69390.35861550.28121435X-RAY DIFFRACTION100
5.6939-6.04940.33661710.29291420X-RAY DIFFRACTION100
6.0494-6.51450.33481580.28741417X-RAY DIFFRACTION100
6.5145-7.16650.32781590.26121449X-RAY DIFFRACTION100
7.1665-8.19520.25011550.23341439X-RAY DIFFRACTION100
8.1952-10.29380.24341620.20131459X-RAY DIFFRACTION100
10.2938-39.11350.31021650.26661490X-RAY DIFFRACTION99
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)
10.6614-1.0816-0.00642.2168-0.36580.3175-0.1016-0.5653-0.57090.26340.32440.33810.3369-0.1714-0.25750.83180.0478-0.45850.75710.25290.963618.466586.738663.8103
20.9547-0.42820.18290.7958-0.28380.97920.0706-0.1436-0.18850.04660.1250.10510.177-0.1443-0.11490.37790.0623-0.29970.3170.07290.18141.5086123.512815.7855
30.1360.27540.180.5880.38690.25530.09010.058-0.2550.07630.1542-0.38430.10420.4408-0.2361.43350.1033-0.84181.4974-0.58472.1233-33.624677.4075-46.8076
41.14870.31230.24220.60240.331.03730.14950.1487-0.3112-0.01470.0475-0.00740.2686-0.0008-0.1350.3348-0.0224-0.30940.3106-0.0380.1947-7.3661121.5783-12.8887
51.9860.17940.11590.3924-0.44071.25820.12440.1167-0.2827-0.10560.018-0.01150.33780.0385-0.12160.62680.1696-0.35950.383-0.09130.519227.8309113.204434.3897
61.64320.36170.41890.87740.1751.32970.18080.5123-0.6496-0.13720.07680.04060.4536-0.1992-0.24220.72-0.1223-0.48290.943-0.09470.9335-36.3453114.5714-29.2723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 81 through 276)
2X-RAY DIFFRACTION2(chain 'A' and resid 409 through 752)
3X-RAY DIFFRACTION3(chain 'B' and resid 81 through 276)
4X-RAY DIFFRACTION4(chain 'B' and resid 409 through 752)
5X-RAY DIFFRACTION5(chain 'A' and resid 277 through 404)
6X-RAY DIFFRACTION6(chain 'B' and resid 277 through 404)

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