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- PDB-8a26: Lysophospholipase PlaA from Legionella pneumophila str. Corby - c... -

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Basic information

Entry
Database: PDB / ID: 8a26
TitleLysophospholipase PlaA from Legionella pneumophila str. Corby - complex with palmitate
ComponentsLysophospholipase A
KeywordsHYDROLASE / phospholipase / virulence
Function / homology
Function and homology information


phosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / hydrolase activity, acting on ester bonds / extracellular region
Similarity search - Function
GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / MALONIC ACID / PALMITIC ACID / Lysophospholipase A
Similarity search - Component
Biological speciesLegionella pneumophila str. Corby (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsDiwo, M.G. / Blankenfeldt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG FL359/6-1/2 (SPP 1580) Germany
German Research Foundation (DFG)DFG FL359/10-1 (SPP 2225) Germany
CitationJournal: Mol.Microbiol. / Year: 2024
Title: Structure-function relationships underpin disulfide loop cleavage-dependent activation of Legionella pneumophila lysophospholipase A PlaA.
Authors: Hiller, M. / Diwo, M. / Wamp, S. / Gutsmann, T. / Lang, C. / Blankenfeldt, W. / Flieger, A.
History
DepositionJun 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysophospholipase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8077
Polymers35,0721
Non-polymers7356
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.919, 82.919, 68.639
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-668-

HOH

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Components

#1: Protein Lysophospholipase A


Mass: 35072.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila str. Corby (bacteria)
Gene: NCTC12000_02489 / Plasmid: pGP172 plaACorby (-SP)* / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A378KFD4, phosphatidylcholine-sterol O-acyltransferase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.2 M (NH4)2SO4, 0.2 M NH4 acetate cryoprotection: 10% (v/v) (2R,3R)-(-)-2,3-butandiole, 2.2 M (NH4)2SO4, 0.2 M NH4 acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.3778 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2018
RadiationMonochromator: double crystal monochromator (Si-111 and Si-113 reflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3778 Å / Relative weight: 1
ReflectionResolution: 1.45→49.62 Å / Num. obs: 48623 / % possible obs: 100 % / Redundancy: 32.7 % / Biso Wilson estimate: 19.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.011 / Rrim(I) all: 0.064 / Net I/σ(I): 33.6 / Num. measured all: 1592101 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.5332.31.33522636870190.8770.2381.3562.9100
4.59-49.6231.20.0351964166510.0050.031127.399.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→49.62 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1762 2371 4.88 %
Rwork0.1545 46219 -
obs0.1555 48590 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 28.608 Å2 / Biso min: 12.77 Å2
Refinement stepCycle: final / Resolution: 1.45→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 115 225 2591
Biso mean--49.37 37.02 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.45-1.480.26791290.263326912820
1.48-1.510.24271340.226127052839
1.51-1.550.24091280.202726662794
1.55-1.590.19511330.18627072840
1.59-1.630.18431580.180827052863
1.63-1.680.20491670.171526432810
1.68-1.730.17131330.168127072840
1.73-1.790.18761310.180927022833
1.79-1.860.19181370.166226872824
1.86-1.950.17851420.160327132855
1.95-2.050.15741250.148327202845
2.05-2.180.17151210.138527432864
2.18-2.350.16591560.141527062862
2.35-2.590.17331250.13527522877
2.59-2.960.18651590.144327252884
2.96-3.730.16741680.145627422910
3.73-49.620.16391250.155329053030
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)
10.7529-0.12690.16021.9522-0.16791.92060.0028-0.01270.10680.023-0.04350.0418-0.14870.11250.02980.1429-0.0024-0.01850.1201-0.02670.1199-23.23241.329312.188
21.87190.96830.11082.99240.03541.2095-0.0060.05520.12360.06690.05140.27140.0072-0.1305-0.04520.13990.0302-0.01940.1301-0.00590.1434-39.013-4.21094.163
30.5999-0.1530.27082.4275-0.89911.62430.03390.029-0.0262-0.0889-0.03560.13160.1230.1138-0.03490.18220.0275-0.00120.1293-0.02140.1348-24.6115-11.47063.179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 125 )A17 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 209 )A126 - 209
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 308 )A210 - 308

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