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- PDB-7byk: Crystal structure of the Legionella pneumophila LegK7 effector kinase -

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Basic information

Entry
Database: PDB / ID: 7byk
TitleCrystal structure of the Legionella pneumophila LegK7 effector kinase
ComponentsLegK7
KeywordsTRANSFERASE / Protein kinase / Legionella pneumophila
Function / homologyProtein kinase-like domain superfamily / Uncharacterized protein / Protein kinase domain containing protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsPark, S.C. / Kim, T.H. / Yoon, S.I.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Activation of the Legionella pneumophila LegK7 Effector Kinase by the Host MOB1 Protein.
Authors: Park, S.C. / Cho, S.Y. / Kim, T.H. / Ko, K.Y. / Song, W.S. / Kang, S.G. / Lee, G.S. / Yoon, S.I.
History
DepositionApr 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LegK7
B: LegK7


Theoretical massNumber of molelcules
Total (without water)110,7982
Polymers110,7982
Non-polymers00
Water36020
1
A: LegK7


Theoretical massNumber of molelcules
Total (without water)55,3991
Polymers55,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LegK7


Theoretical massNumber of molelcules
Total (without water)55,3991
Polymers55,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.996, 74.198, 201.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILE(chain 'A' and (resid 0 through 10 or (resid 11...AA0 - 936 - 99
12GLUGLUILEILE(chain 'A' and (resid 0 through 10 or (resid 11...AA103 - 178109 - 184
13ASNASNPROPRO(chain 'A' and (resid 0 through 10 or (resid 11...AA192 - 469198 - 475
24PROPROILEILE(chain 'B' and (resid 0 through 90 or (resid 91...BB0 - 936 - 99
25GLUGLUILEILE(chain 'B' and (resid 0 through 90 or (resid 91...BB103 - 178109 - 184
26ASNASNPROPRO(chain 'B' and (resid 0 through 90 or (resid 91...BB192 - 469198 - 475

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Components

#1: Protein LegK7


Mass: 55399.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: DI026_09185 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A4T1L9X4, UniProt: Q5ZU83*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 600, imidazole, calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 30648 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 54.82 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 19
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1478 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→29.22 Å / SU ML: 0.3729 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.9822
RfactorNum. reflection% reflection
Rfree0.2526 1442 4.82 %
Rwork0.2047 --
obs0.2071 29917 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.21 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7064 0 0 20 7084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00437234
X-RAY DIFFRACTIONf_angle_d0.67979838
X-RAY DIFFRACTIONf_chiral_restr0.04481105
X-RAY DIFFRACTIONf_plane_restr0.00481284
X-RAY DIFFRACTIONf_dihedral_angle_d13.02534360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.740.31181580.27262771X-RAY DIFFRACTION99.83
2.74-2.850.31121430.26162815X-RAY DIFFRACTION99.73
2.85-2.980.34041300.26192797X-RAY DIFFRACTION99.69
2.98-3.140.32971280.25892807X-RAY DIFFRACTION99.63
3.14-3.340.33661510.24652838X-RAY DIFFRACTION99.9
3.34-3.60.28551270.22482827X-RAY DIFFRACTION99.83
3.6-3.960.2641630.20022843X-RAY DIFFRACTION99.9
3.96-4.530.19891500.16332863X-RAY DIFFRACTION99.97
4.53-5.70.21651480.17252892X-RAY DIFFRACTION99.84
5.7-29.220.2131440.18943022X-RAY DIFFRACTION99.28
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)
13.232695847921.321034204390.6097147615122.47472540417-0.01484404940641.622602431180.1020793468610.0207112399063-0.154686100075-0.143587265681-0.07132294753450.1571157079180.148326493231-0.0560858660136-0.04411586040760.384125120536-0.04845213337340.02613777249250.437327467834-0.0369088520760.347060710449-38.2374826907-2.10740383325-14.5548243273
24.02404295534-1.58109763071-2.166980918341.47231073662.053034784032.02359637001-0.02240029995880.2055546223210.312519939979-0.1748146722010.0824593507442-0.0606629389978-0.05364208081080.171681279621-0.07572606887690.436840180153-0.113072013324-0.02373591779890.4530497774980.07939247677260.40401075512-20.10856464588.20367746318-20.6994342268
31.55145910337-0.282200377401-0.1057890663291.66972577511-0.8386999299692.17727969358-0.05190601279780.472615383679-0.172002525793-0.256475148416-0.0920258580839-0.03309534777670.282249888059-0.06752147266540.1387833069140.522775389259-0.036676231080.03965224080370.736152152254-0.1455322961830.451882422786-7.9859893231-1.29941507068-39.8069042487
43.734636036040.4069298379530.2702913316263.97061335056-0.1252360469742.253012100040.00150194632964-0.3021907558850.377051654895-0.0137800729078-0.0345420400717-0.416105536859-0.1790531236120.3245744728370.04101252329340.451538772166-0.10694480676-0.04324056989350.468664466950.02861825890770.4473690043573.6986083913-32.3373082444-12.2871314
53.26809953711-2.530675009921.713308392714.33228190983-0.688988140661.03509865997-0.0147949764866-0.55661873309-0.447235905901-0.3401056140550.08472160309260.1881270617790.08558782943850.007600758886-0.04077936882060.469205583835-0.0678473289615-0.0296775754260.4764470532180.001131807326280.573113976748-11.4500704775-50.6266513401-16.2964123975
63.54244268061-0.7980284277981.290753727662.37994319105-1.827028644781.67328559306-0.0971130532350.177724707350.09097187077790.05817271506260.06971836802050.133870850689-0.0885179321182-0.1376782057440.009823897838350.415714726951-0.04358741716650.02539941240340.384406221441-0.007247920849770.331342638535-19.1168037729-36.3840560407-24.3393674938
72.477992819850.154456709543-0.07937168270312.29208393793-0.2529242024081.6223485703-0.1935070923421.196749572050.0681929614596-0.5682530804060.2552092435650.01228268961710.165014883781-0.1001254644940.02356379690220.53654352581-0.03779670619270.01189949221450.8277202777550.0418246186070.402881274624-18.0715740003-41.4382338372-43.5545074765
81.2093867666-0.334964835860.5980486445552.04775670597-0.6881413676793.24383376560.04242698972861.405870993720.737872093793-0.3763710188120.357823369260.560782827706-0.302005188641-0.640498209023-0.3025358448250.5750110700430.139324628074-0.04938057252940.957655596020.4017016640490.844103040655-33.3669459956-26.248026083-39.8867133324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 276 )
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 469 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 168 )
5X-RAY DIFFRACTION5chain 'B' and (resid 169 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 322 )
7X-RAY DIFFRACTION7chain 'B' and (resid 323 through 383 )
8X-RAY DIFFRACTION8chain 'B' and (resid 384 through 469 )

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