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- PDB-7lsv: Non-kinase domain of Legionella effector protein kinase LegK2 -

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Basic information

Entry
Database: PDB / ID: 7lsv
TitleNon-kinase domain of Legionella effector protein kinase LegK2
ComponentsCalmodulin-dependent protein kinase
KeywordsPROTEIN BINDING / Bacterial effector / Legionella / kinase
Function / homologyCa2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / ATP binding / MALONATE ION / Calmodulin-dependent protein kinase
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsBeyrakhova, K.A. / van Straaten, K. / Cygler, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-48370 Canada
CitationJournal: To Be Published
Title: Non-kinase domain of Legionella effector protein kinase LegK2
Authors: Beyrakhova, K.A. / van Straaten, K. / Cygler, M.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-dependent protein kinase
B: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3085
Polymers41,1602
Non-polymers1483
Water3,657203
1
A: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6032
Polymers20,5801
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calmodulin-dependent protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7053
Polymers20,5801
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.310, 54.750, 71.650
Angle α, β, γ (deg.)90.000, 107.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Calmodulin-dependent protein kinase


Mass: 20580.193 Da / Num. of mol.: 2
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: legK2, lpg2137 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZTM4, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.4 M Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.58→42.769 Å / Num. obs: 43414 / % possible obs: 98.4 % / Redundancy: 5.732 % / Biso Wilson estimate: 19.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.054 / Χ2: 0.96 / Net I/σ(I): 23.89 / Num. measured all: 248836 / Scaling rejects: 6
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
1.58-1.625.7490.9162.0618219326331690.7121.00997.1
1.62-1.675.7520.7942.3817658317430700.7580.87496.7
1.67-1.715.7310.6782.8217175304529970.8410.74798.4
1.71-1.775.7440.5663.4116808298529260.8730.62498
1.77-1.825.7460.4194.5916232290028250.9370.46297.4
1.82-1.895.7510.3165.8915913283427670.960.34897.6
1.89-1.965.7170.2297.9715139268326480.9770.25398.7
1.96-2.045.7480.15511.5814795260025740.990.17199
2.04-2.135.7420.10516.4414130249324610.9950.11698.7
2.13-2.235.7560.07821.3813545238523530.9970.08798.7
2.23-2.365.7440.05927.612895226822450.9980.06599
2.36-2.55.7410.04931.7912436218521660.9990.05499.1
2.5-2.675.7490.04136.311555202120100.9990.04699.5
2.67-2.885.7270.03343.2610830191418910.9990.03798.8
2.88-3.165.7610.02753.3298111712170310.0399.5
3.16-3.535.7330.0269.8390701585158210.02299.8
3.53-4.085.6980.01583.5779311400139210.01799.4
4.08-55.6990.01491.7668331203119910.01599.7
5-7.075.6020.01582.75515992292110.01699.9
7.07-42.7695.2470.01686.83270253051510.01897.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→42.769 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 2171 5 %
Rwork0.1771 41217 -
obs0.1785 43388 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 27.0045 Å2 / Biso min: 11.83 Å2
Refinement stepCycle: final / Resolution: 1.58→42.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 9 203 2779
Biso mean--68 32.28 -
Num. residues----315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092661
X-RAY DIFFRACTIONf_angle_d1.013590
X-RAY DIFFRACTIONf_chiral_restr0.06388
X-RAY DIFFRACTIONf_plane_restr0.007472
X-RAY DIFFRACTIONf_dihedral_angle_d11.6791633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.61440.29041330.2675252497
1.6144-1.6520.30081330.2496252297
1.652-1.69330.24671340.2345254898
1.6933-1.73910.29391340.2347255297
1.7391-1.79020.24861340.2291254398
1.7902-1.8480.24611350.2091256598
1.848-1.91410.22691330.1938252098
1.9141-1.99070.21441350.184257298
1.9907-2.08130.21671350.1761256099
2.0813-2.1910.18021370.1657259999
2.191-2.32830.17681370.165259899
2.3283-2.5080.18311360.17259199
2.508-2.76040.20751370.1836259699
2.7604-3.15970.21171370.1847260799
3.1597-3.98050.18921390.1522651100
3.9805-42.7690.18731420.1574266999
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)
16.72040.58315.04712.13151.02514.336-0.24740.30690.4858-0.16060.0580.1394-0.73190.28150.22380.1873-0.0271-0.00430.1340.04430.2627-2.85845.81711.448
21.55190.3410.74431.31.15155.0246-0.00650.06610.1636-0.03880.1137-0.0359-0.26070.487-0.10530.1129-0.01270.00580.1923-0.01440.18133.64238.96414.487
32.8779-0.33190.49362.0721-1.10974.8760.0737-0.0869-0.14380.1169-0.0342-0.02750.02680.144-0.02880.08810.0106-0.00130.1295-0.01410.18387.56224.87720.111
42.13560.38360.67151.97921.29044.544-0.0440.26270.2836-0.25630.0648-0.0964-0.34320.28770.00050.1462-0.00860.01280.17450.04290.2103-7.32912.80446.963
52.2806-0.3130.07041.9256-1.5094.9290.03080.0184-0.096-0.0227-0.0192-0.03550.02730.0423-0.01370.06920.01120.00140.0892-0.02590.1853-2.995-3.6654.536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 333:358 )A333 - 358
2X-RAY DIFFRACTION2( CHAIN A AND RESID 359:410 )A359 - 410
3X-RAY DIFFRACTION3( CHAIN A AND RESID 411:489 )A411 - 489
4X-RAY DIFFRACTION4( CHAIN B AND RESID 333:410 )B333 - 410
5X-RAY DIFFRACTION5( CHAIN B AND RESID 411:490 )B411 - 490

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