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- PDB-8dmp: Crystal structure of Legionella pneumophila macrodomain effector MavL -

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Open data


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Basic information

Entry
Database: PDB / ID: 8dmp
TitleCrystal structure of Legionella pneumophila macrodomain effector MavL
ComponentsMavL
KeywordsANTITOXIN / Macrodomain / Effector / Glycohydrolase
Function / homologyUncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsZhang, Z. / Das, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01GM126296 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI148103 United States
CitationJournal: Nat Commun / Year: 2024
Title: Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.
Authors: Zhang, Z. / Fu, J. / Rack, J.G.M. / Li, C. / Voorneveld, J. / Filippov, D.V. / Ahel, I. / Luo, Z.Q. / Das, C.
History
DepositionJul 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MavL
B: MavL
C: MavL
D: MavL
E: MavL
F: MavL
G: MavL
H: MavL


Theoretical massNumber of molelcules
Total (without water)353,4458
Polymers353,4458
Non-polymers00
Water22,9151272
1
A: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: MavL


Theoretical massNumber of molelcules
Total (without water)44,1811
Polymers44,1811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.232, 157.244, 117.621
Angle α, β, γ (deg.)90.000, 96.200, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
MavL


Mass: 44180.664 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1272 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate, 18% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.17→39.31 Å / Num. obs: 176902 / % possible obs: 99.53 % / Redundancy: 4.8 % / Biso Wilson estimate: 39.69 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.93
Reflection shellResolution: 2.17→2.248 Å / Num. unique obs: 17628 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMI
Resolution: 2.17→39.31 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 3894 1.13 %
Rwork0.1873 341022 -
obs0.1876 176690 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.06 Å2 / Biso mean: 45.3528 Å2 / Biso min: 27.55 Å2
Refinement stepCycle: final / Resolution: 2.17→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22812 0 0 1273 24085
Biso mean---47.33 -
Num. residues----2963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.17-2.20.41791410.31981224499
2.2-2.220.29551440.30781240199
2.22-2.250.31181390.29591226699
2.25-2.280.34261410.29241226999
2.28-2.320.27641430.28191224899
2.32-2.350.2951380.27311225199
2.35-2.390.27811410.27091227399
2.39-2.430.2881400.25961224699
2.43-2.470.31971390.25851225099
2.47-2.510.26881420.24881229899
2.51-2.560.27321420.24381222399
2.56-2.610.29611430.23061234099
2.61-2.670.30691410.22931224499
2.67-2.730.22871380.22881233599
2.73-2.80.24731360.22151220699
2.8-2.880.26821380.21361224299
2.88-2.960.25551350.21071215598
2.96-3.060.21171390.21461192496
3.06-3.170.22651370.20671208997
3.17-3.290.23271410.18781229499
3.29-3.440.25331350.18571232299
3.44-3.630.16831410.17391214999
3.63-3.850.16911350.16131218898
3.85-4.150.16161410.13961202897
4.15-4.570.16991360.12921204397
4.57-5.230.14341370.13461188096
5.23-6.580.17521350.15831162193
6.58-39.310.18561360.14871199397
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.34990.7168-0.55054.459-0.25792.668-0.0322-0.01290.0885-0.03020.0740.0558-0.1111-0.0869-0.06050.2280.0081-0.01530.21940.00350.28065.1137-21.631232.2212
21.7690.29310.33731.4283-0.40021.2046-0.02710.1343-0.1725-0.16760.0564-0.11850.0897-0.0303-0.0340.2758-0.02770.00890.2723-0.03240.36610.2982-46.37331.1579
33.9260.30521.68353.6789-0.92394.23270.0751-0.2180.18880.2969-0.16240.2376-0.0159-0.20790.10540.28370.0060.02940.2556-0.00330.3388-0.6609-36.657550.7976
41.4850.02780.76332.4344-0.210.42490.11830.01090.0698-0.2358-0.0329-0.3597-0.2440.1618-0.09070.2461-0.0379-0.01230.2531-0.0020.398512.2862-29.871936.1448
53.6404-1.37361.63744.3744-2.42822.5425-0.01290.05120.22340.15060.0057-0.1055-0.24850.15750.01930.2905-0.0175-0.00090.2674-0.06240.3048-8.20879.686159.8975
60.5701-0.44930.65082.071-1.53131.81060.0005-0.0228-0.007-0.10630.02170.02350.0220.0223-0.05020.2805-0.00880.01240.3622-0.01560.3476-12.7603-2.222961.6648
72.236-0.00471.44242.0041-0.33034.5155-0.02720.20320.1209-0.3269-0.0693-0.2283-0.06920.28630.09310.22120.00720.04340.2260.00210.32372.379-1.982857.7192
81.0806-0.1278-0.16082.0980.14212.15870.0105-0.1310.11-0.0051-0.0416-0.25750.02070.14350.00750.2330.0130.00980.36780.01290.39149.4675-10.917265.5374
93.3297-0.36040.17981.9168-0.98051.4631-0.0776-0.1979-0.29830.03850.0785-0.00140.10080.0714-0.00730.2835-0.00570.0190.3081-0.02230.2968-6.1558-12.189270.7399
101.8627-0.32520.22992.6735-1.11351.7087-0.0181-0.1415-0.0241-0.09930.08740.24040.1098-0.1838-0.11550.28070.00480.02950.4025-0.09110.2847-16.3187-6.727471.1044
112.3964-0.29280.52893.611-0.75672.1329-0.0095-0.0378-0.0791-0.0936-0.0965-0.22510.20610.0690.07830.2970.00720.03780.2503-0.00280.321310.17952.230123.3067
121.76010.638-0.70892.1156-0.34314.7138-0.0462-0.16160.15120.05690.16430.2643-0.2297-0.2969-0.13530.35120.01840.01130.2968-0.01940.448-3.12167.917522.9342
130.9085-0.45360.12911.6526-0.38761.9375-0.0435-0.07780.00210.08660.0321-0.0294-0.0251-0.06520.00860.32710.0040.01580.2557-0.00140.39974.604823.763822.3021
142.6814-0.359-0.45471.137-0.67581.12580.0288-0.13710.33050.14310.0558-0.0724-0.21150.0006-0.07620.39360.00640.00340.2412-0.06240.39234.241133.694526.795
150.6908-0.23640.66321.30910.88491.4784-0.0545-0.09790.0599-0.3043-0.01710.0995-0.14570.03660.0620.35790.01390.01540.27120.0260.37944.316425.342812.5897
161.7547-0.24650.74772.1104-0.52392.57890.02160.10590.0224-0.268-0.059-0.06150.0604-0.05230.07850.3309-0.00580.10230.2367-0.02470.37967.258615.25328.4537
172.94840.1954-0.8762.5025-0.13323.35310.0195-0.04950.03020.0112-0.0043-0.1215-0.0237-0.0458-0.01880.2055-0.0317-0.02760.25840.01620.3-32.1157-35.716319.1572
181.06750.1498-0.09751.7381-0.46951.7469-0.0243-0.00140.0222-0.05160.02710.0218-0.0236-0.2468-0.00450.2785-0.03380.01380.4012-0.04770.3467-45.9335-42.267831.4903
190.2144-0.2287-0.02441.98070.62161.65970.01440.0146-0.08370.0567-0.11860.31350.0391-0.32020.1140.2504-0.06890.01030.5148-0.01320.3865-56.052-42.618235.8591
201.51550.2705-1.19891.2483-0.47352.3991-0.0166-0.1897-0.17440.071-0.0624-0.14090.11740.05150.07810.2959-0.0432-0.00320.3122-0.02560.3564-35.151-48.70434.1443
212.29540.4302-0.42371.2934-0.55342.96950.0546-0.05730.03740.0324-0.06410.0395-0.0587-0.08230.02160.34480.01730.00380.297300.3341-19.7158-19.89650.974
221.0926-0.11410.09793.1656-1.45531.53110.08450.1210.1046-0.0609-0.09890.062-0.16110.06610.02470.40050.03750.03560.31270.00380.4164-10.2489-1.9522-18.1754
231.34090.2813-0.23540.4229-0.14233.5212-0.0183-0.10860.06780.1306-0.0439-0.10110.10350.00110.07580.39230.0323-0.02820.25780.01930.4057-2.4997-14.8725-2.0545
240.51940.36840.23851.8420.76183.2377-0.00880.0398-0.0492-0.08530.0335-0.2051-0.08190.0927-0.02160.3155-0.00680.03190.32670.01410.40124.7763-6.8432-10.7318
251.80860.2259-0.13461.1366-0.00990.4601-0.01470.10180.1133-0.1140.0558-0.0053-0.0525-0.0469-0.05240.37930.02450.01870.26380.0190.3125-11.0108-3.6879-14.3599
261.90660.3614-0.38983.5841-1.1921.9582-0.0532-0.02170.16020.14240.14850.1836-0.1429-0.1568-0.11260.2781-0.0177-0.03750.3111-0.03620.1896-20.7195-9.1794-13.3865
271.1539-0.15180.12532.9297-0.61543.15670.00910.03340.0367-0.1460.0175-0.01420.0116-0.1152-0.02690.236-0.0170.00260.3588-0.02830.3387-51.2148-8.660243.8903
281.3710.00160.37330.9708-0.12421.28630.0136-0.1170.03650.0655-0.0037-0.031-0.0387-0.1761-0.00660.2115-0.02080.00920.3953-0.03010.3012-47.7951-11.460465.1809
291.6881-0.2331-0.1231.5911-0.88353.289-0.0081-0.07490.02230.10990.04330.08120.114-0.2295-0.04840.2740.01540.01140.3343-0.01810.3226-56.6718-1.875720.1076
302.1174-2.03881.29025.0852-0.20361.57490.04180.15780.1749-0.1086-0.0204-0.63210.02830.3614-0.00440.30980.02290.02360.4445-0.02050.374-43.3145-1.446914.028
311.95420.6238-1.45312.9601-2.31912.88250.06050.41460.0849-0.4102-0.00450.10310.1052-0.3166-0.05440.39110.1096-0.04020.4242-0.02230.3401-52.14069.2321-7.6059
324.02120.99370.87114.8250.64454.8336-0.22560.0092-0.1476-0.19030.2008-0.46940.51570.58420.01840.41440.07910.03120.5262-0.00280.4223-40.3325-13.64977.2136
333.4734-2.56412.26845.7762-1.99625.4217-0.1694-0.2301-0.18130.00690.12160.51410.0613-0.87660.01160.33-0.06580.05120.4822-0.06570.3781-58.4251-8.0129-1.4529
349.0386-3.77553.49123.5505-1.67093.7952-0.5629-0.35780.35270.25690.229-0.1448-0.2866-0.54130.25920.38290.01610.03850.4478-0.03020.3375-47.9266-4.5293-6.1602
353.57840.1672-0.91722.8194-0.44113.305-0.09470.3283-0.2612-0.4724-0.06570.19620.4473-0.33930.1560.42740.002-0.03540.381-0.06790.3231-52.2506-10.0484-10.412
362.94150.1454-1.37571.5566-0.081.77370.10560.7679-0.2065-0.2491-0.09180.0768-0.1049-0.44950.02170.60950.067-0.06470.5788-0.08250.406-51.1279-6.7831-18.0416
370.9911.0153-0.65622.40660.83522.0240.09930.1395-0.1072-0.2733-0.03760.0651-0.2061-0.1021-0.03840.34580.0979-0.04440.40720.02410.3667-50.87637.1596-3.9766
382.2039-0.5878-2.77261.87410.24546.26890.22320.03650.46180.0213-0.0386-0.3783-0.51020.498-0.17450.42060.053-0.03040.44420.07920.5439-45.979622.62812.4301
391.7964-0.7129-0.15160.337-0.00192.77220.12170.0031-0.37250.0338-0.09050.26960.2802-0.5756-0.07090.32750.0385-0.02730.4663-0.03340.4649-65.1283-3.066910.5513
404.9944-2.93941.35174.7534-4.71738.5823-0.0711-0.279-0.30230.53240.05920.4137-0.6301-0.6024-0.05120.32170.0216-0.00980.3507-0.09110.3432-32.043426.51445.2259
410.8766-0.61580.50591.5484-1.19881.49990.01720.02810.1452-0.0938-0.04240.0194-0.0265-0.07450.03060.31990.03570.00340.328-0.01290.4084-28.806727.274332.6065
421.6738-0.05590.21785.51690.21571.99320.0511-0.0589-0.06750.2853-0.0472-0.14610.1298-0.28310.00690.2940.0314-0.00060.3923-0.01490.3617-43.913225.270935.1113
430.64670.63890.81031.82880.84082.095-0.0674-0.12510.18010.012-0.05110.2588-0.0521-0.28890.10.30870.07580.01350.47030.01460.4882-51.582432.711926.7807
443.15270.25880.49560.7653-0.7322.443-0.07090.21790.1879-0.1187-0.0311-0.0013-0.1062-0.10440.08240.33550.0630.00910.30440.01060.3338-35.633136.489923.1916
451.7696-0.03070.88411.4878-1.58422.68140.03820.22490.0796-0.0311-0.1342-0.1514-0.14540.1720.1410.3540.04360.00260.2774-0.01270.5057-25.237936.074627.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 127 )A37 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 314 )A128 - 314
3X-RAY DIFFRACTION3chain 'A' and (resid 315 through 375 )A315 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 409 )A376 - 409
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 63 )B41 - 63
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 161 )B64 - 161
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 210 )B162 - 210
8X-RAY DIFFRACTION8chain 'B' and (resid 211 through 292 )B211 - 292
9X-RAY DIFFRACTION9chain 'B' and (resid 293 through 347 )B293 - 347
10X-RAY DIFFRACTION10chain 'B' and (resid 348 through 409 )B348 - 409
11X-RAY DIFFRACTION11chain 'C' and (resid 41 through 99 )C41 - 99
12X-RAY DIFFRACTION12chain 'C' and (resid 100 through 127 )C100 - 127
13X-RAY DIFFRACTION13chain 'C' and (resid 128 through 210 )C128 - 210
14X-RAY DIFFRACTION14chain 'C' and (resid 211 through 292 )C211 - 292
15X-RAY DIFFRACTION15chain 'C' and (resid 293 through 347 )C293 - 347
16X-RAY DIFFRACTION16chain 'C' and (resid 348 through 410 )C348 - 410
17X-RAY DIFFRACTION17chain 'D' and (resid 38 through 127 )D38 - 127
18X-RAY DIFFRACTION18chain 'D' and (resid 128 through 211 )D128 - 211
19X-RAY DIFFRACTION19chain 'D' and (resid 212 through 292 )D212 - 292
20X-RAY DIFFRACTION20chain 'D' and (resid 293 through 410 )D293 - 410
21X-RAY DIFFRACTION21chain 'E' and (resid 42 through 127 )E42 - 127
22X-RAY DIFFRACTION22chain 'E' and (resid 128 through 161 )E128 - 161
23X-RAY DIFFRACTION23chain 'E' and (resid 162 through 210 )E162 - 210
24X-RAY DIFFRACTION24chain 'E' and (resid 211 through 292 )E211 - 292
25X-RAY DIFFRACTION25chain 'E' and (resid 293 through 347 )E293 - 347
26X-RAY DIFFRACTION26chain 'E' and (resid 348 through 412 )E348 - 412
27X-RAY DIFFRACTION27chain 'F' and (resid 41 through 127 )F41 - 127
28X-RAY DIFFRACTION28chain 'F' and (resid 128 through 409 )F128 - 409
29X-RAY DIFFRACTION29chain 'G' and (resid 42 through 99 )G42 - 99
30X-RAY DIFFRACTION30chain 'G' and (resid 100 through 127 )G100 - 127
31X-RAY DIFFRACTION31chain 'G' and (resid 128 through 161 )G128 - 161
32X-RAY DIFFRACTION32chain 'G' and (resid 162 through 185 )G162 - 185
33X-RAY DIFFRACTION33chain 'G' and (resid 186 through 210 )G186 - 210
34X-RAY DIFFRACTION34chain 'G' and (resid 211 through 234 )G211 - 234
35X-RAY DIFFRACTION35chain 'G' and (resid 235 through 270 )G235 - 270
36X-RAY DIFFRACTION36chain 'G' and (resid 271 through 292 )G271 - 292
37X-RAY DIFFRACTION37chain 'G' and (resid 293 through 347 )G293 - 347
38X-RAY DIFFRACTION38chain 'G' and (resid 348 through 383 )G348 - 383
39X-RAY DIFFRACTION39chain 'G' and (resid 384 through 410 )G384 - 410
40X-RAY DIFFRACTION40chain 'H' and (resid 41 through 63 )H41 - 63
41X-RAY DIFFRACTION41chain 'H' and (resid 64 through 161 )H64 - 161
42X-RAY DIFFRACTION42chain 'H' and (resid 162 through 211 )H162 - 211
43X-RAY DIFFRACTION43chain 'H' and (resid 212 through 292 )H212 - 292
44X-RAY DIFFRACTION44chain 'H' and (resid 293 through 347 )H293 - 347
45X-RAY DIFFRACTION45chain 'H' and (resid 348 through 409 )H348 - 409

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