PDB-4o96: 2.60 Angstrom resolution crystal structure of a protein kinase do...

ID or keywords:

Entry

Database: PDB / ID: 4o96

Title

2.60 Angstrom resolution crystal structure of a protein kinase domain of type III effector NleH2 (ECs1814) from Escherichia coli O157:H7 str. Sakai

Components

type III effector protein kinase

Keywords

HYDROLASE / type III effector protein kinase / NleH2 / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / protein kinase fold with N-lobe and C-lobe

Function / homology

Function and homology information

: / protein autophosphorylation / protein phosphorylation
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.6 Å

Authors

Anderson, S.M. / Halavaty, A.S. / Wawrzak, Z. / Kudritska, M. / Skarina, T. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Biochemistry / Year: 2014
Title: Type III Effector NleH2 from Escherichia coli O157:H7 str. Sakai Features an Atypical Protein Kinase Domain.
Authors: Halavaty, A.S. / Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Skarina, T. / Anderson, W.F. / Savchenko, A.

History

Deposition	Jan 1, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2014	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2014	Group: Database references / Structure summary
Revision 1.2	May 21, 2014	Group: Database references
Revision 1.3	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4o96.cif.gz	276.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4o96.ent.gz	228.8 KB	Display	PDB format
PDBx/mmJSON format	4o96.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4o96_validation.pdf.gz	466.4 KB	Display	wwPDB validaton report
Full document	4o96_full_validation.pdf.gz	471.8 KB	Display
Data in XML	4o96_validation.xml.gz	27 KB	Display
Data in CIF	4o96_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/4o96 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/4o96	HTTPS FTP

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Related structure data

Similar structure data	4lrk-5 4lrk-6 1r5z-2 1f4o-d 4id0-d 1ibz-2 5rau-2 5rax-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP91568

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: type III effector protein kinase

B: type III effector protein kinase

C: type III effector protein kinase

D: type III effector protein kinase

hetero molecules

74.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: type III effector protein kinase

B: type III effector protein kinase

hetero molecules

defined by author&software
37.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: type III effector protein kinase

D: type III effector protein kinase

hetero molecules

defined by author&software
37.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	147.252, 147.252, 83.050
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 141 - 303 / Label seq-ID: 4 - 166

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	type III effector protein kinase Mass: 18596.793 Da / Num. of mol.: 4 / Fragment: type III effector protein kinase / Mutation: N-terminal 138 residues were truncated Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: Sakai / Gene: ECs1814, Z6021 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8XAL6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	3.03	59.35
2

Crystal grow

Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Native protein at 10 mg/mL crystallization: 1.6 M NH4 sulphate, 100 mM SPG buffer pH 7.0, 12% glycerol and 1% PEG 2000 MME. cryo conditions: Paratone-N oil , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-D	1	1
SYNCHROTRON	APS	21-ID-G	2	0.97856

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 300 mm CCD	1	CCD	Aug 18, 2012	Mirror
MARMOSAIC 300 mm CCD	2	CCD	Aug 20, 2012	Be-Lenses

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Diamond	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	0.97856	1

Reflection

Resolution: 2.6→50 Å / Num. all: 28323 / Num. obs: 28323 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / B_iso Wilson estimate: 59.8 Å² / R_merge(I) obs: 0.106 / Net I/σ(I): 14.5

Reflection shell

Resolution: 2.6→2.69 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.738 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2767 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHENIX		model building
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.6→46.61 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.909 / SU B: 22.649 / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25288	1434	5.1 %	RANDOM
R_work	0.20812	-	-	-
obs	0.21038	26879	99.04 %	-
all	-	26879	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 59.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.87 Å²	0 Å²	0 Å²
2-	-	2.87 Å²	-0 Å²
3-	-	-	-5.73 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→46.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5136	0	31	170	5337

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	5320
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	5003
X-RAY DIFFRACTION	r_angle_refined_deg	1.669	1.959	7186
X-RAY DIFFRACTION	r_angle_other_deg	1.342	3	11552
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.274	5	660
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.588	25.465	258
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.042	15	955
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.405	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	794
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6094
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1184

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9763	0.06
1	2	B	9763	0.06
2	1	A	9356	0.12
2	2	C	9356	0.12
3	1	A	9318	0.11
3	2	D	9318	0.11
4	1	B	9405	0.12
4	2	C	9405	0.12
5	1	B	9387	0.11
5	2	D	9387	0.11
6	1	C	9542	0.1
6	2	D	9542	0.1

LS refinement shell

Resolution: 2.603→2.67 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.364	105	-
R_work	0.338	1879	-
obs	-	1879	95.75 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.0243	0.1795	-1.2354	1.3014	2.0228	8.3144	0.4494	0.2031	-0.0902	0.1669	-0.0554	-0.231	-0.0249	0.175	-0.394	0.3589	0.1788	0.073	0.1822	0.0412	0.435	168.3717	45.4497	104.1456
2	5.267	-4.0547	2.678	7.246	-2.7482	2.3146	0.1183	0.5251	0.5775	0.0975	-0.0828	-0.2964	0.0311	0.2819	-0.0355	0.1499	0.1178	0.1815	0.2285	0.0814	0.4261	165.1887	49.775	94.7902
3	4.4084	2.877	1.7041	8.2731	0.2799	3.8193	0.5013	0.5572	0.6426	-0.2942	-0.6813	-0.2385	0.2989	0.3998	0.1799	0.2279	0.2296	0.2324	0.3274	0.1451	0.4491	158.0566	52.413	88.5737
4	2.773	0.1538	0.8909	17.9684	3.5257	4.0029	0.411	0.0518	0.4502	-0.4797	-0.6696	0.4968	0.5269	-0.201	0.2586	0.2006	0.0904	0.1506	0.2744	0.0296	0.3996	147.0718	46.8821	87.8648
5	5.1956	0.6703	-0.4192	1.9364	-1.5189	10.3021	0.2123	0.0838	-0.3818	-0.3081	-0.1119	0.0855	0.9326	-0.3599	-0.1004	0.2716	-0.0317	0.0507	0.0354	-0.0251	0.317	144.8696	38.3461	104.6021
6	3.3549	-0.4859	0.1623	3.7314	0.7706	2.8845	-0.1537	0.0512	0.2519	-0.1622	0.0228	0.2152	0.4717	-0.1547	0.131	0.1246	-0.0285	0.0293	0.018	0.042	0.314	146.1696	48.3597	113.4322
7	19.5875	-6.5224	3.8491	4.8909	-4.4028	4.4272	0.3691	1.2586	-1.5555	-0.1763	-0.5308	0.1889	0.3056	0.581	0.1617	0.4235	0.2957	0.0762	0.4369	-0.0207	0.3819	163.9011	40.1777	115.4683
8	14.9491	-8.9199	2.9187	15.5363	-2.8469	2.2212	-0.4598	-0.1334	0.8921	0.4993	0.3945	-0.3078	0.0997	0.5193	0.0653	0.0685	0.091	0.0159	0.2326	-0.0166	0.3388	159.0055	55.7007	118.3189
9	1.1779	-1.0678	1.8832	6.0228	2.4294	9.1103	0.0852	0.4001	0.0861	-0.7575	-0.0393	0.0784	-0.7588	0.0648	-0.046	0.3403	0.1552	-0.0086	0.4525	0.0505	0.4156	179.549	21.1184	96.7634
10	7.003	-3.123	4.0409	4.314	-0.1037	9.1694	0.1248	0.4931	0.0296	-0.5224	-0.1736	-0.1493	-0.6577	0.764	0.0489	0.2774	0.023	0.0649	0.1491	0.0341	0.3033	182.5752	24.1994	100.6806
11	4.3744	0.0906	-0.3527	2.0327	0.8538	11.2301	0.0422	-0.0103	0.4074	-0.1366	0.1561	-0.4541	-0.7545	2.021	-0.1984	0.0997	-0.0536	0.0203	0.5143	-0.0288	0.3699	193.8282	20.5432	111.953
12	14.0014	-1.4622	-0.9485	5.0803	0.2316	9.6935	0.2095	-0.0781	-0.455	0.3397	-0.0305	0.3333	0.2616	0.2644	-0.179	0.0982	0.1229	-0.0003	0.2423	-0.0202	0.1788	187.0971	13.1707	120.3342
13	2.9934	2.5921	-0.7549	3.1184	0.8801	9.2583	0.2404	-0.4214	-0.1372	0.4244	0.0123	0.2531	1.3922	-0.6413	-0.2528	0.4146	-0.1064	-0.0712	0.6045	0.1986	0.5627	174.8121	4.2017	113.8046
14	8.7376	-1.9545	-3.2843	4.5789	1.4441	10.9011	0.2624	-0.2563	-0.3602	0.0894	-0.047	0.3796	1.5091	-0.3181	-0.2155	0.624	-0.04	-0.1202	0.1843	0.0297	0.3991	174.9769	-0.175	108.4455
15	3.2804	-0.0208	0.2306	2.997	1.1663	12.1403	0.2027	0.0548	-0.4902	0.2202	0.1087	-0.1036	2.1877	1.2343	-0.3114	0.6945	0.4462	-0.1045	0.3112	-0.093	0.3672	186.3067	-3.356	97.5696
16	13.7055	-3.0889	4.2871	6.1003	-1.2201	9.8084	0.0055	0.0487	0.5288	-0.0601	0.1212	-0.044	0.5358	0.4499	-0.1266	0.2308	0.2498	-0.041	0.3457	-0.0854	0.2429	184.7299	6.6072	89.2846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	141 - 183
2	X-RAY DIFFRACTION	2	A	184 - 232
3	X-RAY DIFFRACTION	3	A	233 - 273
4	X-RAY DIFFRACTION	4	A	274 - 303
5	X-RAY DIFFRACTION	5	B	141 - 194
6	X-RAY DIFFRACTION	6	B	195 - 267
7	X-RAY DIFFRACTION	7	B	268 - 281
8	X-RAY DIFFRACTION	8	B	282 - 303
9	X-RAY DIFFRACTION	9	C	141 - 186
10	X-RAY DIFFRACTION	10	C	187 - 222
11	X-RAY DIFFRACTION	11	C	223 - 272
12	X-RAY DIFFRACTION	12	C	273 - 303
13	X-RAY DIFFRACTION	13	D	141 - 184
14	X-RAY DIFFRACTION	14	D	185 - 222
15	X-RAY DIFFRACTION	15	D	223 - 272
16	X-RAY DIFFRACTION	16	D	273 - 303

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