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- PDB-8a24: Lysophospholipase PlaA from Legionella pneumophila str. Corby - i... -

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Basic information

Entry
Database: PDB / ID: 8a24
TitleLysophospholipase PlaA from Legionella pneumophila str. Corby - iodide soak
ComponentsLysophospholipase A
KeywordsHYDROLASE / phospholipase / virulence / single anomalous diffraction
Function / homologyphosphatidylcholine-sterol O-acyltransferase / phosphatidylcholine-sterol O-acyltransferase activity / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / IODIDE ION / Lysophospholipase A
Function and homology information
Biological speciesLegionella pneumophila str. Corby (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.36 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)36,72214
Polymers35,0721
Non-polymers1,65013
Water1,11762
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)81.852, 81.852, 68.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.88 Å3/Da / Density % sol: 34.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 14.7% (w/v) PEG3350, 1% (w/v) PEG 1K, 0.5% (w/v) PEG200, 8.9% (v/v) Tacsimate pH 5, 200 mM NH4I, 1 mM CaCl2 and 1 mM MgCl2; cryoprotection and iodide soaking for iodide-SAD: 10% (v/v) (2R,3R) ...Details: 14.7% (w/v) PEG3350, 1% (w/v) PEG 1K, 0.5% (w/v) PEG200, 8.9% (v/v) Tacsimate pH 5, 200 mM NH4I, 1 mM CaCl2 and 1 mM MgCl2; cryoprotection and iodide soaking for iodide-SAD: 10% (v/v) (2R,3R)-(-)-2,3-butandiole, 16% (w/v) PEG3350, 6% (v/v) Tacsimate pH 5, 920 mM NH4I

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2018
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.36→70.89 Å / Num. obs: 11147 / % possible obs: 100 % / Redundancy: 38.3 % / Biso Wilson estimate: 45.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.031 / Rrim(I) all: 0.192 / Net I/σ(I): 21.4 / Num. measured all: 427303
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
2.36-2.4937.71.8216010915930.8440.2971.8462.5100
7.48-70.8935.90.08142953980.9990.0130.08174.299.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHENIX1.20_4459refinement
PDB_EXTRACT3.27data extraction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.36→70.89 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 547 4.92 %
Rwork0.2281 10577 -
obs0.2306 11124 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.37 Å2 / Biso mean: 59.1416 Å2 / Biso min: 29.58 Å2
Refinement stepCycle: final / Resolution: 2.36→70.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 13 62 2275
Biso mean--90.47 53.03 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.36-2.60.28861190.273525962715
2.6-2.980.32321490.233526112760
2.98-3.750.25651620.229226042766
3.75-70.890.27961170.218427662883
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)
11.4813-0.11420.22234.9398-0.99644.3837-0.0294-0.00030.1684-0.0384-0.05630.0344-0.3560.1490.08820.29710.0104-0.03520.3084-0.05680.2785-22.07440.733612.3119
23.61661.45490.82063.42430.5413.19170.09330.1391-0.09640.2677-0.00270.32520.0698-0.2979-0.07980.29490.0393-0.04170.32450.00450.3228-38.3063-4.29254.6458
31.3722-0.52981.19114.2174-1.78444.46790.00620.1832-0.0773-0.4448-0.0988-0.11760.44580.2850.04240.33750.0738-0.0210.2711-0.03540.2617-24.3485-10.68792.7154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 125 )A20 - 125
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 207 )A126 - 207
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 308 )A208 - 308

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