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- PDB-6zti: Phospholipase PlaB from Legionella pneumophila in complex with th... -

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Basic information

Entry
Database: PDB / ID: 6zti
TitlePhospholipase PlaB from Legionella pneumophila in complex with thio-NAD
ComponentsPlaB phospholipase
KeywordsHYDROLASE / phospholipase / alpha/beta hydrolase / virulence / infectious disease
Function / homologyAlpha/Beta hydrolase fold / nucleotide binding / THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE / PlaB phospholipase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsDiwo, M.G. / Flieger, A. / Blankenfeldt, W.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)FL359/4-2/3 Germany
German Research Foundation (DFG)281361126/GRK2223 Germany
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB.
Authors: Diwo, M. / Michel, W. / Aurass, P. / Kuhle-Keindorf, K. / Pippel, J. / Krausze, J. / Wamp, S. / Lang, C. / Blankenfeldt, W. / Flieger, A.
#1: Journal: Biorxiv / Year: 2020
Title: NAD(H)-mediated tetramerization controls the activity of Legionella pneumophila phospholipase PlaB
Authors: Diwo, M. / Michel, W. / Aurass, P. / Kuhle-Keindorf, K. / Pippel, J. / Krausze, J. / Lang, C. / Blankenfeldt, W. / Flieger, A.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.journal_id_ISSN / _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: PlaB phospholipase
B: PlaB phospholipase
C: PlaB phospholipase
D: PlaB phospholipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,35216
Polymers221,5484
Non-polymers5,80412
Water30,6621702
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26070 Å2
ΔGint-109 kcal/mol
Surface area67470 Å2
Unit cell
Length a, b, c (Å)75.831, 90.725, 92.790
Angle α, β, γ (deg.)78.440, 90.260, 75.410
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PlaB phospholipase


Mass: 55386.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: plaB, NCTC12000_01733 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A378K488
#2: Chemical
ChemComp-SND / THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 679.491 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1702 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 8.33% glycerol, 10.8% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.21233 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21233 Å / Relative weight: 1
ReflectionResolution: 1.81→46.91 Å / Num. obs: 161898 / % possible obs: 76 % / Redundancy: 12.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.39 / Rpim(I) all: 0.11 / Rrim(I) all: 0.41 / Net I/σ(I): 7.3
Reflection shellResolution: 1.81→1.95 Å / Rmerge(I) obs: 2.38 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8096 / CC1/2: 0.53 / Rpim(I) all: 0.82 / Rrim(I) all: 2.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
PHENIXdev_3922refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: xxxx

Resolution: 1.81→46.91 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 8002 4.95 %
Rwork0.1856 153733 -
obs0.188 161735 75.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.17 Å2 / Biso mean: 23.4137 Å2 / Biso min: 3.62 Å2
Refinement stepCycle: final / Resolution: 1.81→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14808 0 619 1702 17129
Biso mean--15.66 30.12 -
Num. residues----1861
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.830.2658140.23821491632
1.83-1.850.2889210.23433393605
1.85-1.880.297450.254772677111
1.88-1.90.3352870.25521391147821
1.9-1.920.31471050.26882075218031
1.92-1.950.27021390.25372741288041
1.95-1.980.28591770.24883436361351
1.98-2.010.28962110.25193943415459
2.01-2.040.28832380.24564378461665
2.04-2.070.28412530.2464695494869
2.07-2.110.28922590.23335194545376
2.11-2.150.26452860.21595531581783
2.15-2.190.28313080.20226077638590
2.19-2.230.26073340.2026465679996
2.23-2.280.28993900.21666478686897
2.28-2.330.26262920.19056629692198
2.33-2.390.23463340.19056664699898
2.39-2.460.24283250.19266651697698
2.46-2.530.24643360.18356617695398
2.53-2.610.24323600.18386638699898
2.61-2.70.21543100.18676677698798
2.7-2.810.2283360.17496680701699
2.81-2.940.21883500.16666648699899
2.94-3.10.22513470.17516681702899
3.1-3.290.20613350.16256708704399
3.29-3.540.20263620.15496672703499
3.54-3.90.20013510.15396701705299
3.9-4.460.2083640.14867277091100
4.46-5.620.19493570.158366997056100
5.62-46.910.2343760.22767237099100
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)
11.21460.38060.21611.62410.12710.64410.0851-0.0598-0.26060.0531-0.0382-0.07670.2910.19970.0530.17850.0822-0.04280.1291-0.03370.12910.2969-46.05656.684
20.6144-0.07040.13850.9596-0.0260.69530.02590.0173-0.04540.00980.0206-0.01930.07250.0791-0.00950.03060.02450.00150.0922-0.01350.04423.3926-29.9498-6.4792
30.24070.43540.48640.70020.81951.3171-0.01580.01790.0782-0.134-0.03960.0162-0.29850.01390.04290.1144-0.00650.02610.1233-0.01090.10064.0587-3.1787-3.8803
41.7159-0.329-0.32121.67440.02251.27580.05740.13190.249-0.0348-0.028-0.1003-0.2560.09810.04680.1457-0.05260.03030.11090.00290.113310.441615.247324.0758
50.83030.0724-0.1160.86490.00910.66720.03470.0130.0443-0.0058-0.0008-0.0249-0.07250.0208-0.01930.03990.0012-0.01360.0622-0.01730.03643.4396-1.285437.1249
60.1633-0.3962-0.40290.88350.82811.323-0.02190.0251-0.02940.1417-0.0275-0.02230.30540.02370.03080.11040.0061-0.02120.1083-0.02220.11053.956-27.890634.5244
71.47670.1245-0.42851.6001-0.30870.91110.0883-0.02420.2452-0.0453-0.0990.0751-0.3168-0.06860.02340.15370.08020.00650.119-0.01460.11-38.79628.9107-5.1469
80.661-0.0433-0.05350.9585-0.10480.67530.03490.00760.0424-0.0467-0.01310.0154-0.0554-0.0644-0.01880.03830.0094-0.01040.0807-0.01080.0391-31.9885-11.3981-10.4166
90.09040.1442-0.32010.3638-0.38931.96340.00840.0277-0.0724-0.0219-0.02740.050.35530.0234-0.00240.1101-0.0117-0.01650.1054-0.00150.1127-32.3997-34.77133.1856
101.6953-0.27670.58221.3773-0.22311.18460.03680.0013-0.23140.0929-0.03540.06760.2682-0.11120.00970.1665-0.06650.00350.1107-0.0060.1082-38.9447-39.976535.7442
110.92670.0760.02651.0395-0.03930.95150.0412-0.0362-0.02690.0607-0.00470.04050.1023-0.0805-0.02590.045-0.02340.00250.0788-0.00790.0346-33.2915-22.439142.4097
120.5571-0.31390.54110.8523-0.53190.60210.02550.10910.0819-0.0599-0.0227-0.08790.0422-0.11010.00220.0535-0.0180.02520.11520.01130.0503-26.3572-3.011532.8713
130.1358-0.21720.43150.2962-0.51551.97540.0049-0.02680.02220.0330.00450.0124-0.287-0.0036-0.03560.09950.01690.00710.093-0.00180.0938-32.60523.591327.8092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 99 )A0 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 374 )A100 - 374
3X-RAY DIFFRACTION3chain 'A' and (resid 375 through 474 )A375 - 474
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 99 )B0 - 99
5X-RAY DIFFRACTION5chain 'B' and (resid 100 through 374 )B100 - 374
6X-RAY DIFFRACTION6chain 'B' and (resid 375 through 474 )B375 - 474
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 99 )C0 - 99
8X-RAY DIFFRACTION8chain 'C' and (resid 100 through 374 )C100 - 374
9X-RAY DIFFRACTION9chain 'C' and (resid 375 through 474 )C375 - 474
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 99 )D0 - 99
11X-RAY DIFFRACTION11chain 'D' and (resid 100 through 334 )D100 - 334
12X-RAY DIFFRACTION12chain 'D' and (resid 335 through 374 )D335 - 374
13X-RAY DIFFRACTION13chain 'D' and (resid 375 through 474 )D375 - 474

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