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- PDB-8dmr: Legionella macrodomain effector MavL R370A in complex with ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 8dmr
TitleLegionella macrodomain effector MavL R370A in complex with ADP-ribose
ComponentsMavL
KeywordsANTITOXIN / Complex / Macrodomain / Metaeffector
Function / homologyChem-AR6 / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0037
Polymers44,0951
Non-polymers9096
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.557, 95.557, 54.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MavL


Mass: 44094.547 Da / Num. of mol.: 1 / Mutation: R370A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSJ1

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Non-polymers , 6 types, 304 molecules

#2: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.99 Å3/Da / Density % sol: 58.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M ammonium sulfate

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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: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→42.21 Å / Num. obs: 41115 / % possible obs: 99.65 % / Redundancy: 4.6 % / Biso Wilson estimate: 34.85 Å2 / CC1/2: 0.998 / Net I/σ(I): 23.61
Reflection shellResolution: 1.86→1.927 Å / Num. unique obs: 4087 / CC1/2: 0.781

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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

6omi


Resolution: 1.86→42.21 Å / SU ML: 0.1787 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2849
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1798 2031 4.94 %
Rwork0.1506 39043 -
obs0.152 41074 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.04 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 57 298 3214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122995
X-RAY DIFFRACTIONf_angle_d1.21924075
X-RAY DIFFRACTIONf_chiral_restr0.0616444
X-RAY DIFFRACTIONf_plane_restr0.0089525
X-RAY DIFFRACTIONf_dihedral_angle_d15.1539434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.28041220.23922558X-RAY DIFFRACTION98.24
1.9-1.950.22011490.20712589X-RAY DIFFRACTION99.89
1.95-20.2371590.2122572X-RAY DIFFRACTION100
2-2.060.22511120.18582599X-RAY DIFFRACTION99.93
2.06-2.130.20071350.17462596X-RAY DIFFRACTION99.71
2.13-2.20.23641320.1722553X-RAY DIFFRACTION98.71
2.2-2.290.19881380.16512606X-RAY DIFFRACTION99.89
2.29-2.40.20941540.16122580X-RAY DIFFRACTION100
2.4-2.520.22131130.16492609X-RAY DIFFRACTION99.82
2.52-2.680.21291660.1642584X-RAY DIFFRACTION99.93
2.68-2.890.18521210.172646X-RAY DIFFRACTION99.86
2.89-3.180.20641260.16532604X-RAY DIFFRACTION99.42
3.18-3.640.18231170.14052645X-RAY DIFFRACTION99.78
3.64-4.580.13131550.11452617X-RAY DIFFRACTION99.6
4.58-42.210.14951320.13732685X-RAY DIFFRACTION98.91
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)
12.7600447953-1.31926844435-0.4787715411852.565056624920.4217699458222.994688494070.0742909187354-0.2619236341060.2679293932950.09531209456890.331217708543-0.6104574395440.211656770980.520270991427-0.3420711296010.2572486263150.0162169856311-0.04608181976330.280241397123-0.1307136726870.45702295843114.921649555933.2311807589-2.30790362744
23.09693463127-1.02777880141-0.06759504689842.96558283720.7043149141142.442060007430.06177134740810.138889929597-0.0471176367623-0.125517196470.075842958093-0.2842055920210.2997657196640.0827986416345-0.1458420688870.329078137306-0.00243526403579-0.00835102610730.211406028527-0.0306199884160.2364653115595.207813972526.4782436456-6.83253535546
32.521725609120.422424305138-0.2160101005562.268747711680.4543530791922.267836433190.142993684264-0.196429250984-0.3173371459650.715720194820.15844559076-0.2220284742241.056747533930.239753199482-0.2639241136780.6315579672010.0684308216821-0.1086548629340.2558466859130.003601256710370.3451662845563.1228401064920.451393472611.54762261
42.04840464958-0.7592093141780.1175968344614.8499874297-0.3325370507212.79461177065-0.00802659522266-0.0423701597880.06430071478510.08685023278240.0600767935562-0.1032494670910.0699501167545-0.192890394741-0.04073000392120.235304569914-0.005411827224460.001218628674910.243054124379-0.03003118114170.20582315829-3.3126912865935.90676212064.92041525788
52.710494740260.350738786688-0.03034661315315.29767495564-0.4790947719633.732325817230.0402198269684-0.1642806919660.06579433370340.2974782374610.0193526106339-0.0216139819678-0.0199778769019-0.228768280142-0.04939497954360.2596412491130.02461637633750.01480439906990.28380198795-0.02138977271070.253646847232-6.6174319465540.346101985510.152481171
61.43881351639-1.00088382014-0.5236895991393.326234417160.9586030035492.563623095030.07697856668510.1127180279830.01843975647810.0763984821214-0.1292362825740.4889556268550.0101588553188-0.637133358180.07201168998680.233667241763-0.02711001239530.0001777174435130.3499750677510.007124363396570.316816219953-13.119576901937.01328474862.17636869106
74.23804572535-0.320785614239-0.6521479182673.59506444273-0.3542672267013.556985482410.04163510190810.582743781904-0.185206201794-0.584972268689-0.1299902308760.3342081518130.234932915493-0.4503348220150.09826583470520.419349233547-0.0427138480849-0.08696925013540.400795659549-0.05341479647210.29626884723-10.065723866226.6761115395-16.2215622161
84.33177482532-1.27515498937-0.87086947053.241092955350.9139052865664.598594645030.1570714500910.3071345325710.0432114897773-0.4498871878190.334838082435-0.697404516510.02834264121340.380262810821-0.4486260651370.335428544090.04707020949630.07942316188190.1597844418420.08692443486350.2554925261766.5489876384832.4864925615-10.7939383732
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 64 )37 - 641 - 28
22chain 'A' and (resid 65 through 160 )65 - 16029 - 125
33chain 'A' and (resid 161 through 185 )161 - 185126 - 150
44chain 'A' and (resid 186 through 235 )186 - 235151 - 200
55chain 'A' and (resid 236 through 263 )236 - 263201 - 228
66chain 'A' and (resid 264 through 321 )264 - 321229 - 286
77chain 'A' and (resid 322 through 369 )322 - 369287 - 334
88chain 'A' and (resid 370 through 409 )370 - 409335 - 374

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