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- PDB-5clr: Crystal structure of LegK4_APO Kinase -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5clr
TitleCrystal structure of LegK4_APO Kinase
ComponentsLegK4
KeywordsTRANSFERASE / Legionella / Bacterial effectors / serine/threonine kinase / type IV secretion system
Function / homology
Function and homology information


symbiont-mediated perturbation of host translation / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.706 Å
AuthorsFlayhan, A. / Terradot, L.
CitationJournal: Sci Rep / Year: 2015
Title: The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase.
Authors: Flayhan, A. / Berge, C. / Bailo, N. / Doublet, P. / Bayliss, R. / Terradot, L.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LegK4
B: LegK4


Theoretical massNumber of molelcules
Total (without water)103,1582
Polymers103,1582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-4 kcal/mol
Surface area36080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.820, 154.820, 87.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein LegK4


Mass: 51578.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (strain Lens) (bacteria)
Gene: lpl0262 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5WZW9
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% (w/v) PEG 4000, 20% glycerol, 0.1 M MOPS/HEPES pH 7.5, 5 mM Hexaammine cobalt (III) chloride.

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: si [111] crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.7→44.693 Å / Num. obs: 13215 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.239 / Net I/σ(I): 13.79
Reflection shellResolution: 3.706→3.838 Å / Redundancy: 2.47 % / Rmerge(I) obs: 1.419 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.706→44.693 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3107 651 4.93 %Random selection
Rwork0.2821 ---
obs0.2835 13211 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.706→44.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 0 0 5596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025686
X-RAY DIFFRACTIONf_angle_d0.5387649
X-RAY DIFFRACTIONf_dihedral_angle_d13.5542117
X-RAY DIFFRACTIONf_chiral_restr0.02908
X-RAY DIFFRACTIONf_plane_restr0.003935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7057-3.99170.35781270.33422476X-RAY DIFFRACTION100
3.9917-4.39310.37021390.29192469X-RAY DIFFRACTION100
4.3931-5.0280.28781310.27582488X-RAY DIFFRACTION100
5.028-6.33190.33641260.32772516X-RAY DIFFRACTION100
6.3319-44.69590.27041280.24562611X-RAY DIFFRACTION100

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