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- PDB-4lrk: Bacterial Effector NleH2 Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 4lrk
TitleBacterial Effector NleH2 Kinase Domain
ComponentsEffector NleH2
KeywordsTRANSFERASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / kinase fold / bacterial effector kinase
Function / homology
Function and homology information


: / protein autophosphorylation / protein phosphorylation
Similarity search - Function
Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
T3SS secreted effector NleH
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.274 Å
AuthorsCygler, M. / Grishin, A.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Structure / Year: 2014
Title: NleH defines a new family of bacterial effector kinases.
Authors: Grishin, A.M. / Cherney, M. / Anderson, D.H. / Phanse, S. / Babu, M. / Cygler, M.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Effector NleH2
B: Effector NleH2
C: Effector NleH2
D: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)74,7924
Polymers74,7924
Non-polymers00
Water5,386299
1
A: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)18,6981
Polymers18,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)18,6981
Polymers18,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)18,6981
Polymers18,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)18,6981
Polymers18,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Effector NleH2

B: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)37,3962
Polymers37,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area16120 Å2
MethodPISA
6
C: Effector NleH2
D: Effector NleH2


Theoretical massNumber of molelcules
Total (without water)37,3962
Polymers37,3962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-13 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.288, 145.288, 83.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Effector NleH2


Mass: 18697.898 Da / Num. of mol.: 4 / Fragment: Kinase Domain (UNP residues 140-303)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ECs1814, nleh2, Z6021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q8XAL6, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES 6.5, 30% PEG 5000MME, 200 mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
177.21
277.21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCLSI 08ID-110.97949
SYNCHROTRONCLSI 08ID-120.97871
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDMay 16, 2012
RAYONIX MX-3002CCDJun 6, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRRORSINGLE WAVELENGTHMx-ray1
2dcm WITH CRYO-COOLED 1ST CRYSTAL SAGITALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRRORSADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.978711
ReflectionRedundancy: 11.6 % / Number: 365200 / Rmerge(I) obs: 0.145 / Χ2: 1.71 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 31562 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785099.810.0814.25110.4
5.386.7810010.0963.22911.2
4.75.3810010.0892.31811.3
4.274.710010.0942.27911.4
3.974.2710010.1122.17311.5
3.733.9710010.1141.87911.6
3.553.7310010.1251.80711.6
3.393.5510010.1531.85411.7
3.263.3910010.1841.57611.7
3.153.2610010.2391.47911.7
3.053.1510010.3221.39211.7
2.963.0510010.3991.27211.7
2.892.9610010.4661.20411.7
2.822.8910010.6171.1411.8
2.752.8210010.7231.12311.8
2.692.7510010.8781.0911.7
2.642.6910010.961.06711.7
2.592.6410011.06511.8
2.542.5910011.03711.7
2.52.5410011.03911.7
ReflectionResolution: 2.27→50 Å / Num. obs: 41406 / % possible obs: 99.7 %

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
DENZOdata reduction
AutoSolphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: SAD / Resolution: 2.274→45.944 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 2000 4.83 %
Rwork0.1737 --
obs0.1758 41366 99.4 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.27 Å2 / Biso mean: 38.2873 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: LAST / Resolution: 2.274→45.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5082 0 0 299 5381
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)
11.85360.09830.20161.75810.53422.0648-0.06190.04820.17080.0008-0.05410.009-0.32180.0630.07390.1199-0.0131-0.04010.06150.03470.160973.847528.159555.1241
21.76650.0174-0.39270.7478-0.10461.3-0.0304-0.347-0.12340.0919-0.1035-0.0548-0.21490.20860.07790.1984-0.0986-0.10840.16390.00630.230385.457924.9067-11.2408
32.42990.12130.10061.6914-1.57892.8938-0.09490.1157-0.2631-0.1932-0.0669-0.24570.06770.39880.12450.2654-0.17870.02660.3714-0.00950.196290.366335.590223.8418
42.0735-0.54530.80811.4559-0.57574.4814-0.1691-0.2496-0.08410.13510.24050.2734-0.546-0.7143-0.03420.3564-0.014-0.01280.47530.02450.258771.249744.000219.5421
5-0.2-0.13670.01680.10090.0880.256-0.0146-0.02190.0006-0.0272-0.02140.0282-0.10190.0802-0.05030.0941-0.0942-0.02390.1618-0.00360.116580.574228.0420.2955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 142:303 )A142 - 303
2X-RAY DIFFRACTION2( CHAIN B AND RESID 142:303 )B142 - 303
3X-RAY DIFFRACTION3( CHAIN C AND RESID 142:303 )C142 - 303
4X-RAY DIFFRACTION4( CHAIN D AND RESID 142:303 )D142 - 303
5X-RAY DIFFRACTION5( CHAIN A AND RESID 401:512 ) OR ( CHAIN C AND RESID 401:441 ) OR ( CHAIN B AND RESID 401:518 ) OR ( CHAIN D AND RESID 401:428 )A401 - 512
6X-RAY DIFFRACTION5( CHAIN A AND RESID 401:512 ) OR ( CHAIN C AND RESID 401:441 ) OR ( CHAIN B AND RESID 401:518 ) OR ( CHAIN D AND RESID 401:428 )C401 - 441
7X-RAY DIFFRACTION5( CHAIN A AND RESID 401:512 ) OR ( CHAIN C AND RESID 401:441 ) OR ( CHAIN B AND RESID 401:518 ) OR ( CHAIN D AND RESID 401:428 )B401 - 518
8X-RAY DIFFRACTION5( CHAIN A AND RESID 401:512 ) OR ( CHAIN C AND RESID 401:441 ) OR ( CHAIN B AND RESID 401:518 ) OR ( CHAIN D AND RESID 401:428 )D401 - 428

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