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- PDB-6zth: Phospholipase PlaB from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 6zth
TitlePhospholipase PlaB from Legionella pneumophila
ComponentsPlaB phospholipase
KeywordsHYDROLASE / phospholipase / alpha/beta hydrolase / virulence / infectious disease
Function / homologyAlpha/Beta hydrolase fold / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PlaB phospholipase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PlaB phospholipase
B: PlaB phospholipase
C: PlaB phospholipase
D: PlaB phospholipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,48112
Polymers224,1744
Non-polymers5,3078
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25800 Å2
ΔGint-74 kcal/mol
Surface area67910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.806, 170.578, 93.485
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PlaB phospholipase


Mass: 56043.441 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 77.8 mM NaSCN, 1.67% glycerol, 5.44% PEG400, 11.6% 2-propanol, 4.11% tacsimate , seeding required

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→49.24 Å / Num. obs: 104870 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.099 / Rrim(I) all: 0.263 / Net I/σ(I): 5.9 / Num. measured all: 728092 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.341.2463563051400.7240.5081.3471.599.9
12.6-49.240.08745026570.9970.0360.09416.898.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIXdev_3922refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→49.24 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4127 5247 5.01 %
Rwork0.3638 99380 -
obs0.3662 104627 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.3 Å2 / Biso mean: 40.2617 Å2 / Biso min: 2.72 Å2
Refinement stepCycle: final / Resolution: 2.3→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14903 0 560 543 16006
Biso mean--34.06 25.89 -
Num. residues----1880
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 (%)
2.3-2.330.40891630.385132693432100
2.33-2.350.43021870.383732903477100
2.35-2.380.38371820.381933083490100
2.38-2.410.43821770.382432803457100
2.41-2.440.36941860.377633373523100
2.44-2.480.41391660.381732813447100
2.48-2.510.41491700.378733353505100
2.51-2.550.47241730.369832903463100
2.55-2.590.40721770.375933293506100
2.59-2.630.43771730.383533083481100
2.63-2.680.44621750.37633263501100
2.68-2.730.42361740.374832963470100
2.73-2.780.51171730.390733023475100
2.78-2.840.42941760.368533113487100
2.84-2.90.47281720.37143287345999
2.9-2.970.45141740.368833023476100
2.97-3.040.42881760.378333463522100
3.04-3.120.42711740.362733223496100
3.12-3.210.40781740.362432903464100
3.21-3.320.44231750.35733333508100
3.32-3.440.40691750.358533243499100
3.44-3.570.39691730.347233083481100
3.57-3.740.40151770.343933313508100
3.74-3.930.36761720.347132803452100
3.93-4.180.38241750.337733253500100
4.18-4.50.41221770.330533593536100
4.5-4.950.40291740.346633203494100
4.95-5.670.38331750.354633193494100
5.67-7.140.36371750.3933353510100
7.14-49.240.4211770.40163337351498
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)
10.58830.33780.12050.737-0.28682.2642-0.03870.4011-0.1686-0.078-0.1438-0.23150.15320.55110.09310.54240.2414-0.05640.5112-0.04990.3257-37.1292-9.8213-14.8392
20.1778-0.2262-0.27420.6569-0.68633.945-0.0634-0.09560.0767-0.04610.053-0.1572-0.08120.26630.07410.21150.0519-0.07340.4364-0.09650.4243-40.72690.9709-16.8102
30.20920.2406-0.46660.6646-0.70442.2750.08150.0574-0.0484-0.029-0.08140.2171-0.0771-0.1023-0.06690.37480.22170.03350.4873-0.10460.385-45.30392.4767-28.5478
40.7856-0.4816-0.4921.04770.31680.84210.08720.1434-0.0073-0.2414-0.0946-0.1241-0.0639-0.02820.03830.37440.2173-0.08930.3844-0.14380.4758-0.8549-47.0127-52.2784
50.5676-0.08910.11450.72140.23270.44120.1076-0.0162-0.0197-0.1249-0.06520.02520.18880.05050.05940.28620.21950.00150.3782-0.16580.2921-5.9039-32.1616-54.9633
60.2929-0.19060.0920.47710.17510.1010.05210.3897-0.1264-0.1450.0905-0.06710.06540.09940.0130.2410.24020.05020.4675-0.09770.2827-5.6429-24.6911-65.8591
70.35570.04180.36691.30120.9911.8879-0.07570.01580.0821-0.2223-0.08940.0133-0.49170.2506-0.03660.20580.15540.01980.2962-0.0690.3044-7.6028-2.0987-53.1113
80.76690.14750.2060.0502-0.06390.4103-0.05690.13790.2702-0.057-0.05450.1097-0.24050.0341-0.42890.57190.2617-0.02620.4402-0.18950.29230.78459.9209-22.3798
90.71620.4512-0.44980.5322-0.01940.86020.05770.18480.07650.18570.0015-0.2630.01-0.25360.03540.31660.12680.00930.3746-0.21680.3181-7.1042-8.078-17.9537
100.55770.5938-0.11620.89920.06010.8210.0026-0.11130.06250.012-0.08470.1057-0.1424-0.11160.00550.4140.1708-0.04660.3101-0.08650.252-8.4186-10.0642-8.4179
110.4656-0.1453-0.13890.45540.80712.1982-0.10310.0616-0.08890.0739-0.10750.0287-0.031-0.05310.1160.45420.17620.03430.4056-0.07670.4787-5.4818-36.8355-29.1011
120.6142-0.1247-0.83511.8430.2511.19030.01430.08440.0022-0.10860.00240.274-0.4288-0.2007-0.13550.31880.2515-0.0420.5-0.13680.4354-48.637811.8602-52.1045
130.74690.27610.12481.4226-0.24710.26910.04010.26460.1044-0.05940.00010.0851-0.0569-0.1777-0.05620.31250.1537-0.00680.3678-0.07070.256-42.7709-2.4409-62.2871
140.1870.04340.0110.3354-0.36831.11970.02470.07240.0029-0.02370.0089-0.0390.3517-0.20150.02320.21950.1502-0.02380.3832-0.08720.3551-40.8021-29.6869-54.0568
151.72050.0568-0.88361.8153-0.25712.0106-0.13720.2158-0.24680.08070.00180.05410.4144-0.14560.16450.50420.2063-0.01380.5345-0.13770.3694-50.0857-43.6752-22.6434
160.59620.4260.05190.35780.18070.5260.1090.1449-0.1439-0.3081-0.03310.0517-0.12550.12330.03360.30480.2021-0.07770.3588-0.10840.3762-37.8845-30.0307-18.5353
170.64860.37690.1510.69640.03470.95290.13040.0583-0.05290.0269-0.10510.01960.18150.0487-0.01690.40320.13680.0220.2872-0.02510.2511-44.2947-28.9097-7.7664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 335 through 389 )D335 - 389
2X-RAY DIFFRACTION2chain 'D' and (resid 390 through 423 )D390 - 423
3X-RAY DIFFRACTION3chain 'D' and (resid 424 through 474 )D424 - 474
4X-RAY DIFFRACTION4chain 'A' and (resid -2 through 74 )A-2 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 207 )A75 - 207
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 362 )A208 - 362
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 474 )A363 - 474
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 121 )B0 - 121
9X-RAY DIFFRACTION9chain 'B' and (resid 122 through 245 )B122 - 245
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 404 )B246 - 404
11X-RAY DIFFRACTION11chain 'B' and (resid 405 through 474 )B405 - 474
12X-RAY DIFFRACTION12chain 'C' and (resid 0 through 98 )C0 - 98
13X-RAY DIFFRACTION13chain 'C' and (resid 99 through 324 )C99 - 324
14X-RAY DIFFRACTION14chain 'C' and (resid 325 through 474 )C325 - 474
15X-RAY DIFFRACTION15chain 'D' and (resid -2 through 113 )D-2 - 113
16X-RAY DIFFRACTION16chain 'D' and (resid 114 through 207 )D114 - 207
17X-RAY DIFFRACTION17chain 'D' and (resid 208 through 334 )D208 - 334

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