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- PDB-6vvc: Legionella pneumophila Lpg2603 kinase -

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Basic information

Entry
Database: PDB / ID: 6vvc
TitleLegionella pneumophila Lpg2603 kinase
ComponentsDot/Icm T4SS effector
KeywordsTRANSFERASE / phosphorylation / kinase
Function / homologyDrrA phosphatidylinositol 4-phosphate binding domain / DrrA, PI4P binding domain superfamily / DrrA phosphatidylinositol 4-phosphate binding domain / host cell cytoplasmic vesicle / regulation of GTPase activity / small GTPase binding / nucleotide binding / Dot/Icm T4SS effector / DrrA phosphatidylinositol 4-phosphate binding domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Park, B.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R00DK099254 United States
Welch FoundationI-1911 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: ALegionellaeffector kinase is activated by host inositol hexakisphosphate.
Authors: Sreelatha, A. / Nolan, C. / Park, B.C. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S.
History
DepositionFeb 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: Dot/Icm T4SS effector
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9046
Polymers37,5931
Non-polymers3105
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint11 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.961, 62.961, 176.407
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-525-

HOH

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Components

#1: Protein Dot/Icm T4SS effector / Lpg2603


Mass: 37593.328 Da / Num. of mol.: 1 / Fragment: UNP residues 10-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_13135, DI056_05180, DI105_03620 / Plasmid: ppSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta
References: UniProt: A0A2S6F2W2, UniProt: Q5ZSB6*PLUS, Transferases; Transferring phosphorus-containing groups
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.68 Å3/Da / Density % sol: 54.19 % / Mosaicity: 0.545 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% w/v PEG3350, 0.2 M lithium chloride, 0.03 M sodium chloride, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 / Details: monochromator
RadiationMonochromator: sagittally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24083 / % possible obs: 98.4 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.035 / Rrim(I) all: 0.09 / Χ2: 0.962 / Net I/σ(I): 9 / Num. measured all: 141650
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.30.5710640.7230.3620.6821.0790.9
2.14-2.182.70.55111300.7540.3390.6531.02993.3
2.18-2.223.10.50911120.7870.2950.5931.05394.6
2.22-2.263.50.48911740.8160.270.5631.08696.9
2.26-2.314.10.44811880.880.2340.5091.04498.4
2.31-2.374.60.40811690.9160.2040.4591.01599.1
2.37-2.4250.40411870.9170.1920.451.02597.3
2.42-2.4960.38512040.9620.1690.4221.011100
2.49-2.566.70.35912070.9660.1480.3891.004100
2.56-2.657.10.32711980.9730.130.3531.00499.9
2.65-2.747.20.27412290.9830.1080.2951.012100
2.74-2.857.10.22312030.9880.0890.2411.002100
2.85-2.986.60.15912110.990.0660.1730.9599.9
2.98-3.147.60.1212390.9940.0460.1290.95899.9
3.14-3.337.40.08712190.9960.0340.0930.91999.9
3.33-3.597.30.06912160.9970.0270.0740.903100
3.59-3.956.80.05512460.9970.0220.060.86599.6
3.95-4.527.60.0512590.9980.0190.0530.82799.8
4.52-5.76.90.0512720.9970.020.0540.83299.6
5.7-506.70.05513560.9960.0240.061.01799

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-3000data scaling
SHELXEphasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→31.48 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9919
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1998 8.69 %random
Rwork0.1768 ---
obs0.1798 23005 94.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 20 176 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00242390
X-RAY DIFFRACTIONf_angle_d0.58343231
X-RAY DIFFRACTIONf_chiral_restr0.0425329
X-RAY DIFFRACTIONf_plane_restr0.0037417
X-RAY DIFFRACTIONf_dihedral_angle_d15.2011899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.29151100.22681132X-RAY DIFFRACTION74.19
2.15-2.210.30291290.20041251X-RAY DIFFRACTION80.65
2.21-2.280.22911300.19181348X-RAY DIFFRACTION86.43
2.28-2.350.24771330.19071425X-RAY DIFFRACTION90.32
2.35-2.440.22191290.17311377X-RAY DIFFRACTION87.1
2.44-2.530.2431480.17661570X-RAY DIFFRACTION99.59
2.53-2.650.21931480.17471555X-RAY DIFFRACTION99.88
2.65-2.790.2131520.17931575X-RAY DIFFRACTION100
2.79-2.960.20431490.18151590X-RAY DIFFRACTION99.94
2.96-3.190.19741490.17721610X-RAY DIFFRACTION100
3.19-3.510.1981570.16951602X-RAY DIFFRACTION99.94
3.51-4.020.20041460.16311593X-RAY DIFFRACTION99.66
4.02-5.060.1821580.15231645X-RAY DIFFRACTION99.83
5.06-31.480.21211600.1971734X-RAY DIFFRACTION99.37
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)
13.014176321870.7902053199240.5782138514932.036565060080.3301114593270.7261209454710.01144027671870.2389371118831.265566690690.4293134010260.03351717731370.553954996005-0.302028322323-0.00468172981750.08900238298950.4339367345670.0943668961405-0.06955607661180.499998317633-0.1345092163020.518182813907-15.677281254848.99627080972.20172921373
23.322427150650.9358990414660.1951497620823.819252342110.6191319993392.60525370459-0.167147354835-0.629832259316-0.01823340678430.4430564456990.04845077355570.04562233594880.0107799851682-0.1472788838350.08739795080640.2501671311220.08290105739060.001879140567670.322444454098-0.0153162177750.15837288229-19.501995909528.5546401624-1.26433897049
33.12118629556-0.398183062962-1.098065197680.7906120444730.2560274698722.57931747683-0.01104983800990.02111198990070.1554793120640.02396263923940.0651459462130.0100299583249-0.0340883368501-0.112164718265-0.04401068698350.1402140404910.00502295490244-0.002711294089660.140573769341-0.002860201238880.182263300133-17.396292446226.9152529742-18.796718752
43.50125166546-1.53880836054-0.7298328466481.672449503640.1904643197972.9017890419-0.198148910894-0.200496923895-0.07312711403080.2692714238810.03221873745220.1767111287360.0241613494549-0.1744951312990.08908254764320.126499745769-0.01575552526670.02831150697080.144581824188-0.007351142753490.141273798003-17.512398167723.9732699777-18.627929553
52.487567236460.246682954882-0.3776929794584.87814704161-2.018449470013.0681549827-0.1337103513070.0942876615173-0.1790806913990.1777878201960.2768663125560.1376400910950.252942667666-0.276865398641-0.09632968639170.187596763841-0.008618023761720.05420370185370.147031223336-0.01130243578870.181259661952-11.022835419515.3841786853-25.6683602982
62.130415284210.325598651048-0.5333779679741.04638656807-0.8415926498272.94025131573-0.02229892883670.217482991861-0.160390989896-0.04985075910040.0495842841559-0.002287866431090.2298725987910.0451598447382-0.03739996044540.1816654020890.004171609629340.01441590575320.179984643411-0.03627314441650.19338794317-0.60781243449417.1495012684-31.8502958943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 142 )
3X-RAY DIFFRACTION3chain 'A' and (resid 143 through 210 )
4X-RAY DIFFRACTION4chain 'A' and (resid 211 through 238 )
5X-RAY DIFFRACTION5chain 'A' and (resid 239 through 259 )
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 321 )

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