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- PDB-8a25: Lysophospholipase PlaA from Legionella pneumophila str. Corby - c... -

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Basic information

Entry
Database: PDB / ID: 8a25
TitleLysophospholipase PlaA from Legionella pneumophila str. Corby - complex with PEG fragment
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 / IODIDE ION / MALONIC ACID / TRIETHYLENE GLYCOL / Lysophospholipase A
Similarity search - Component
Biological speciesLegionella pneumophila str. Corby (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)35,6476
Polymers35,0721
Non-polymers5755
Water3,027168
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)82.238, 82.238, 68.447
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-508-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 173 molecules

#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-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.91 Å3/Da / Density % sol: 35.44 %
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, 200 mM NH4I

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.3778 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: 1.3778 Å / Relative weight: 1
ReflectionResolution: 1.73→71.22 Å / Num. obs: 27102 / % possible obs: 95.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 26.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.015 / Rrim(I) all: 0.065 / Net I/σ(I): 28.6 / Num. measured all: 519071
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
1.73-1.8319.71.1928043640890.8330.2741.2232.5100
5.48-71.2219.10.0251883298510.0060.02599.499.9

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→71.22 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1833 1313 4.85 %
Rwork0.1578 25760 -
obs0.159 27073 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.75 Å2 / Biso mean: 37.949 Å2 / Biso min: 17.77 Å2
Refinement stepCycle: final / Resolution: 1.73→71.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 59 168 2490
Biso mean--54.67 39.99 -
Num. residues----289
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.73-1.80.28281370.233829643101100
1.8-1.880.2671580.214629313089100
1.88-1.980.2381460.201729553101100
1.98-2.110.19531100.16392466257683
2.11-2.270.19181340.15982371250581
2.27-2.50.20891490.14829723121100
2.5-2.860.18841670.157529603127100
2.86-3.60.17791690.153929953164100
3.6-71.220.14951430.144431463289100
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)
12.8357-0.1479-0.58473.1009-0.34973.83180.0357-0.09960.238-0.1702-0.04770.0573-0.24730.3103-0.00930.2445-0.0101-0.020.1988-0.03750.2005-23.04192.82388.2379
22.2631-1.6192-0.09994.36841.84463.4792-0.0812-0.05510.00860.33660.1122-0.16140.33370.4576-0.03780.2470.03-0.02360.2642-0.0160.178-18.7783-9.30820.256
31.4188-0.5384-0.83733.5557-0.10513.2690.04610.01020.1297-0.1302-0.0306-0.1998-0.17410.56740.00350.246-0.0095-0.02890.3268-0.01640.207-15.77350.04356.4335
41.5768-2.7971.16246.02380.30016.6734-0.0581-0.3465-0.65770.6648-0.21050.92870.4626-0.79930.22330.3418-0.01690.08140.3351-0.0950.391-35.6011-3.807317.7124
53.1953-0.0231-1.03964.10380.31844.81730.0408-0.04350.3030.1531-0.04180.1721-0.71960.0052-0.02070.31380.0124-0.03470.1815-0.03840.2924-28.647311.289312.0177
63.38781.0922-0.345.2326-0.21652.1019-0.0057-0.14130.18880.4712-0.00340.5250.0042-0.2522-0.00830.2140.0438-0.01730.1956-0.04810.2292-40.5368-1.79398.8052
71.76981.98070.82228.35941.02042.2879-0.01340.0231-0.0135-0.1390.01270.25620.2013-0.07210.02610.18810.0347-0.01160.2065-0.03210.2214-32.8509-7.81853.7263
82.2954-0.5980.89625.4547-0.6442.72-0.18490.22310.4729-0.35430.02350.8018-0.1498-0.308-0.0630.23470.0309-0.11470.2268-0.00910.331-41.2942-3.5804-0.8455
92.2277-1.26040.73676.2701-0.11471.6435-0.03320.3034-0.0118-0.492-0.09580.47960.03860.04830.11050.31990.005-0.02950.20480.02710.1954-28.6957-4.8573-5.8832
103.0005-0.36170.10494.73760.49131.49540.0921-0.4161-0.2525-0.08640.11050.49040.96040.2258-0.06080.45650.0584-0.06820.213-0.00340.3409-27.2501-22.411310.7582
112.3871-1.21830.97585.231-0.08793.90390.00480.0116-0.28260.0271-0.16650.28920.37430.32580.12730.33210.0475-0.01950.2567-0.0230.2638-22.6265-19.761812.0422
121.9662-1.25250.16993.0612-0.60183.93330.12710.28860.2597-0.4023-0.2022-0.074-0.29990.63870.02820.3006-0.0177-0.0230.27580.01720.2012-19.09770.1955-3.711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 35 )A20 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 55 )A36 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 81 )A56 - 81
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 101 )A82 - 101
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 125 )A102 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 159 )A126 - 159
7X-RAY DIFFRACTION7chain 'A' and (resid 160 through 184 )A160 - 184
8X-RAY DIFFRACTION8chain 'A' and (resid 185 through 209 )A185 - 209
9X-RAY DIFFRACTION9chain 'A' and (resid 210 through 234 )A210 - 234
10X-RAY DIFFRACTION10chain 'A' and (resid 235 through 255 )A235 - 255
11X-RAY DIFFRACTION11chain 'A' and (resid 256 through 284 )A256 - 284
12X-RAY DIFFRACTION12chain 'A' and (resid 285 through 308 )A285 - 308

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