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- PDB-6yvg: Crystal structure of MesI (Lpg2505) from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 6yvg
TitleCrystal structure of MesI (Lpg2505) from Legionella pneumophila
ComponentsMesI (Lpg2505)
KeywordsPROTEIN BINDING
Function / homologyProtein of unknown function DUF5630 / Family of unknown function (DUF5630) / IODIDE ION / Ankyrin repeat protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsMachtens, D.A. / Willerding, J.M. / Eschenburg, S. / Reubold, T.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the metaeffector MesI (Lpg2505) from Legionella pneumophila.
Authors: Machtens, D.A. / Willerding, J.M. / Eschenburg, S. / Reubold, T.F.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 1, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MesI (Lpg2505)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,35210
Polymers34,2751
Non-polymers1,0779
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint2 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.960, 56.910, 70.920
Angle α, β, γ (deg.)90.000, 99.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MesI (Lpg2505)


Mass: 34275.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Gene: lpg2505 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZSL2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM ammonium iodide, 20 % w/v PEG3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 210.98
SYNCHROTRONSOLEIL PROXIMA 222.0837
SYNCHROTRONSOLEIL PROXIMA 231.0386
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELMay 30, 2018
DECTRIS EIGER X 9M2PIXELMay 30, 2018
DECTRIS EIGER X 9M3PIXELJul 30, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
22.08371
31.03861
ReflectionResolution: 2.2→44.14 Å / Num. obs: 15667 / % possible obs: 99.6 % / Redundancy: 3.529 % / Biso Wilson estimate: 59.807 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.082 / Χ2: 1.063 / Net I/σ(I): 9.74 / Num. measured all: 107228
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.33.5230.961.2513283383437700.6221.13298.3
2.3-2.43.6330.71.9311545317131780.7690.822100
2.4-2.53.5790.5152.679524267326610.840.60799.6
2.5-2.73.4650.34.3114815428642760.9480.35699.8
2.7-33.5150.1727.515905453045250.9780.20499.9
3-3.53.5320.0913.3115614442544210.9920.10699.9
3.5-43.6330.0619.779039249224880.9950.07199.8
4-53.4010.04822.168451249024850.9950.05799.8
5-63.5380.04322.723817108210790.9970.05199.7
6-83.3860.04123.6829838828810.9960.04999.9
8-103.7110.03427.5911543133110.9990.03999.4
10-123.7290.03228.034811291290.9990.037100
12-153.620.0328.1533392920.9980.035100
15-203.4550.0326.0119055550.9980.036100
20-44.142.6860.04524.099441350.9940.05585.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→44.14 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 783 5 %
Rwork0.185 14864 -
obs0.1872 15647 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.13 Å2 / Biso mean: 62.941 Å2 / Biso min: 32.85 Å2
Refinement stepCycle: final / Resolution: 2.2→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 12 45 2272
Biso mean--82.63 59.34 -
Num. residues----274
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.340.35131290.287424442573
2.34-2.520.29051300.247724572587
2.52-2.770.28011300.233724842614
2.77-3.170.28791290.23124592588
3.17-40.24051310.177124872618
4-44.140.17551340.14925332667

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