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- PDB-6aoj: Crystal structure of Legionella pneumophila effector Ceg4 with N-... -

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Basic information

Entry
Database: PDB / ID: 6aoj
TitleCrystal structure of Legionella pneumophila effector Ceg4 with N-terminal yeast Hog1p sequence
ComponentsCeg4
KeywordsHYDROLASE / Effector / Legionella pneumophila / infection / HAD-like phosphatase / alpha/beta protein / phosphotyrosine
Function / homologyHAD-like superfamily / metal ion binding / membrane / Dot/Icm T4SS effector
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å
AuthorsStogios, P.J. / Nocek, B. / Cuff, M.E. / Evdokimova, E. / Egorova, O. / Yim, V. / Di Leo, R. / Savchenko, A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: TheLegionella pneumophilaeffector Ceg4 is a phosphotyrosine phosphatase that attenuates activation of eukaryotic MAPK pathways.
Authors: Quaile, A.T. / Stogios, P.J. / Egorova, O. / Evdokimova, E. / Valleau, D. / Nocek, B. / Kompella, P.S. / Peisajovich, S. / Yakunin, A.F. / Ensminger, A.W. / Savchenko, A.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Ceg4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9853
Polymers24,9261
Non-polymers602
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.970, 75.923, 47.911
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

#1: Protein Ceg4


Mass: 24925.596 Da / Num. of mol.: 1 / Fragment: UNP residues 1-208
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: lpg0096 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5ZZB5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 M bis-Tris pH 6.5, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 20881 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.031 / Net I/σ(I): 39.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 992 / CC1/2: 0.961 / Rpim(I) all: 0.149 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AOK

6aok


Resolution: 1.902→32.529 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.51
RfactorNum. reflection% reflectionSelection details
Rfree0.1927 1044 5 %RANDOM
Rwork0.1624 ---
obs0.164 20876 96.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.902→32.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 2 245 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091781
X-RAY DIFFRACTIONf_angle_d0.9542410
X-RAY DIFFRACTIONf_dihedral_angle_d21.898672
X-RAY DIFFRACTIONf_chiral_restr0.064249
X-RAY DIFFRACTIONf_plane_restr0.006321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9024-2.00270.28251400.22152674X-RAY DIFFRACTION91
2.0027-2.12810.24321490.19492826X-RAY DIFFRACTION98
2.1281-2.29240.21941510.18262866X-RAY DIFFRACTION98
2.2924-2.5230.23941510.18072860X-RAY DIFFRACTION98
2.523-2.88790.24861520.18872883X-RAY DIFFRACTION98
2.8879-3.63770.18421520.16392889X-RAY DIFFRACTION98
3.6377-32.53380.15351490.13672834X-RAY DIFFRACTION95
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)
19.94767.033-7.70695.0072-5.4046.0297-0.105-0.07230.3545-0.32680.51540.3101-0.8980.1626-0.35660.59590.05980.06920.6513-0.050.4771.304226.471380.8392
22.7311-1.2329-1.04635.60151.65143.81920.0427-0.0096-0.11880.1203-0.07780.1010.1917-0.01440.03810.2334-0.0356-0.00640.26860.04130.315281.919415.970550.4273
36.2851-1.81410.45476.6885-2.04418.21280.1357-0.77620.33460.781-0.00780.116-0.25670.1222-0.10520.391-0.12390.0250.3168-0.05760.355782.869432.022761.7051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -5:3 )A-5 - 3
2X-RAY DIFFRACTION2( CHAIN A AND RESID 4:145 )A4 - 145
3X-RAY DIFFRACTION3( CHAIN A AND RESID 148:205 )A148 - 205

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