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- PDB-6omi: Crystal structure of the Legionella effector protein MavL -

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Basic information

Entry
Database: PDB / ID: 6omi
TitleCrystal structure of the Legionella effector protein MavL
ComponentsMavL
KeywordsHYDROLASE / ADP-ribosyltransferase (ART) / macrodomain / Secreted bacterial effector protein
Function / homology: / Macrodomain effector MavL / ADP-D-ribose binding / host cell cytoplasm / extracellular region / BROMIDE ION / Macrodomain effector MavL domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.643 Å
AuthorsCygler, M. / Voth, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)412613 Canada
CitationJournal: To Be Published
Title: Crystal Structure of the Legionella Effector protein MavL
Authors: Cygler, M. / Voth, K.
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _refine_hist.d_res_low

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4305
Polymers133,2703
Non-polymers1602
Water25214
1
A: MavL
B: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9273
Polymers88,8472
Non-polymers801
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-20 kcal/mol
Surface area27770 Å2
MethodPISA
2
C: MavL
hetero molecules

C: MavL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0064
Polymers88,8472
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area2330 Å2
ΔGint-21 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.619, 138.009, 108.523
Angle α, β, γ (deg.)90.00, 92.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-501-

BR

21C-605-

HOH

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Components

#1: Protein MavL


Mass: 44423.336 Da / Num. of mol.: 3 / Fragment: residues 42-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2526 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZSJ1
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.993054 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.993054 Å / Relative weight: 1
ReflectionResolution: 2.643→48.77 Å / Num. obs: 41740 / % possible obs: 99.26 % / Redundancy: 1.998 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.53
Reflection shellResolution: 2.643→2.738 Å / Rmerge(I) obs: 1.387 / Num. unique obs: 4058

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.643→45.14 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1249 2.99 %
Rwork0.2114 --
obs0.2126 41718 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.643→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 2 14 8108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028296
X-RAY DIFFRACTIONf_angle_d0.56411319
X-RAY DIFFRACTIONf_dihedral_angle_d14.3534841
X-RAY DIFFRACTIONf_chiral_restr0.0431240
X-RAY DIFFRACTIONf_plane_restr0.0041489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.643-2.74860.37611380.33414359X-RAY DIFFRACTION97
2.7486-2.87370.37231280.31294482X-RAY DIFFRACTION99
2.8737-3.02520.38071500.28764509X-RAY DIFFRACTION99
3.0252-3.21470.30781410.27924449X-RAY DIFFRACTION99
3.2147-3.46280.30751330.25154481X-RAY DIFFRACTION99
3.4628-3.81120.25061410.22094517X-RAY DIFFRACTION100
3.8112-4.36240.2571410.18134537X-RAY DIFFRACTION100
4.3624-5.49490.19271360.17734540X-RAY DIFFRACTION100
5.4949-48.770.2291410.19674595X-RAY DIFFRACTION100
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)
14.1686-0.63350.73893.1318-0.12463.98530.2808-0.0151-0.53670.06040.0169-0.28130.6960.4112-0.22110.91540.4024-0.18110.6239-0.15530.863566.173842.81718.6459
23.21860.02990.92192.2782-0.22393.0124-0.0906-0.23380.246-0.2383-0.23580.2112-0.5479-0.74890.28210.73370.4361-0.02190.8609-0.13320.610851.69573.585226.6803
33.1610.30490.06572.7249-0.50793.04120.5005-1.63050.01770.3946-0.3461-0.23660.0977-0.1324-0.14920.5643-0.17350.01341.4148-0.00350.733682.805172.077166.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 41 through 404)
2X-RAY DIFFRACTION2(chain 'B' and resid 40 through 404)
3X-RAY DIFFRACTION3(chain 'C' and resid 40 through 403)

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