PDB-8oyq: Structure of the Histidine Kinase CheA ATP-Binding domain in comp...

ID or keywords:

Entry

Database: PDB / ID: 8oyq

Title

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK13

Components

Chemotaxis protein CheA

Keywords

SIGNALING PROTEIN /

inhibitor /

Transferase

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity /

chemotaxis / protein domain specific binding /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Adhav, A. / Marina, A.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK13
Authors: Adhav, A. / Marina, A.

History

Deposition	May 5, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8oyq.cif.gz	350.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8oyq.ent.gz	219.1 KB	Display	PDB format
PDBx/mmJSON format	8oyq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oy/8oyq ftp://data.pdbj.org/pub/pdb/validation_reports/oy/8oyq	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (5) #183 - Mar 2015 Phototropin similarity (5)

Deposited unit

B: Chemotaxis protein CheA

A: Chemotaxis protein CheA

hetero molecules

42.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Chemotaxis protein CheA

hetero molecules

defined by author
Evidence: In silico studies followed by biophysical methods like Microscale thermophoresis were used to assess the binding of the fragment to CheA.
21.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Chemotaxis protein CheA

hetero molecules

defined by author
21.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.962, 59.201, 66.259
Angle α, β, γ (deg.)	90.000, 97.162, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 5 - 189 / Label seq-ID: 5 - 189

Dom-ID	Auth asym-ID	Label asym-ID
1	A	B
2	B	A

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Chemotaxis protein CheA / Mass: 21079.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: cheA, TM_0702 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56310, histidine kinase
#2: Chemical	ChemComp-W6T / quinazolin-2-amine Mass: 145.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₇N₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.89 Å³/Da / Density % sol: 35.05 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG 8000 30% Ammonium acetate 0.6 M Sodium acetate 0.065 M ph 4.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97951 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 1.8→65.74 Å / Num. obs: 28452 / % possible obs: 97.3 % / Redundancy: 6.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / R_pim(I) all: 0.029 / R_rim(I) all: 0.054 / Net I/σ(I): 23.1
Reflection shell	Resolution: 1.8→1.847 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.172 / Num. unique obs: 2050 / CC_1/2: 0.988 / R_pim(I) all: 0.109 / R_rim(I) all: 0.205

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0411	refinement
REFMAC	5.8.0411	refinement
SCALA		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→44.031 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.94 / WR_factor R_free: 0.248 / WR_factor R_work: 0.199 / SU B: 5.527 / SU ML: 0.083 / Average fsc free: 0.9682 / Average fsc work: 0.9807 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2259	1375	4.835 %	RANDOM
R_work	0.1845	27061	-	-
all	0.186	-	-	-
obs	-	28436	97.127 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.563 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.401 Å²	-0 Å²	-0.224 Å²
2-	-	0.124 Å²	0 Å²
3-	-	-	0.324 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→44.031 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2680	0	22	53	2755

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	2730
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2720
X-RAY DIFFRACTION	r_angle_refined_deg	2.071	1.641	3666
X-RAY DIFFRACTION	r_angle_other_deg	0.693	1.576	6281
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.213	5	340
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.631	5	18
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.151	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.105	10	527
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.177	10	119
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	424
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3116
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	560
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	548
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	2536
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	1392
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1648
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.135	0.2	60
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.38	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.304	0.2	126
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.201	0.2	20
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.004	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.888	1.906	1375
X-RAY DIFFRACTION	r_mcbond_other	2.875	1.906	1375
X-RAY DIFFRACTION	r_mcangle_it	3.821	3.396	1710
X-RAY DIFFRACTION	r_mcangle_other	3.822	3.397	1711
X-RAY DIFFRACTION	r_scbond_it	5.41	2.615	1355
X-RAY DIFFRACTION	r_scbond_other	5.41	2.616	1355
X-RAY DIFFRACTION	r_scangle_it	8.052	4.456	1956
X-RAY DIFFRACTION	r_scangle_other	8.05	4.456	1957
X-RAY DIFFRACTION	r_lrange_it	9.588	26.446	3004
X-RAY DIFFRACTION	r_lrange_other	9.59	26.102	3002
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.145	0.05	4982

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	B	X-RAY DIFFRACTION	Local ncs	0.14546	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.14546	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.235	103	0.186	2050	0.188	2167	0.965	0.979	99.3539	0.172
1.847-1.897	0.264	102	0.175	1966	0.179	2085	0.959	0.982	99.1846	0.166
1.897-1.952	0.232	89	0.172	1931	0.174	2045	0.97	0.982	98.7775	0.163
1.952-2.012	0.218	96	0.162	1840	0.164	1958	0.975	0.985	98.8764	0.159
2.012-2.078	0.261	97	0.181	1808	0.186	1914	0.961	0.98	99.5298	0.178
2.078-2.151	0.243	89	0.18	1781	0.183	1890	0.964	0.981	98.9418	0.18
2.151-2.232	0.225	92	0.183	1656	0.185	1764	0.968	0.98	99.093	0.185
2.232-2.323	0.261	61	0.174	1140	0.178	1733	0.957	0.982	69.3018	0.179
2.323-2.426	0.225	83	0.17	1562	0.173	1661	0.973	0.983	99.0367	0.179
2.426-2.544	0.211	87	0.172	1477	0.174	1603	0.975	0.984	97.5671	0.18
2.544-2.681	0.232	64	0.176	1423	0.178	1499	0.968	0.982	99.1995	0.189
2.681-2.843	0.231	65	0.169	1345	0.172	1418	0.971	0.983	99.4358	0.186
2.843-3.038	0.2	62	0.193	1293	0.193	1360	0.976	0.978	99.6324	0.218
3.038-3.28	0.261	58	0.195	1186	0.198	1258	0.961	0.976	98.8871	0.222
3.28-3.591	0.211	53	0.209	1070	0.21	1149	0.973	0.972	97.7372	0.237
3.591-4.012	0.228	54	0.185	973	0.187	1052	0.967	0.979	97.6236	0.218
4.012-4.626	0.218	46	0.175	881	0.178	935	0.972	0.982	99.1444	0.213
4.626-5.65	0.202	37	0.19	745	0.191	793	0.98	0.982	98.6129	0.241
5.65-7.926	0.247	25	0.23	580	0.231	626	0.97	0.973	96.6454	0.285
7.926-44.031	0.13	12	0.181	354	0.179	366	0.981	0.978	100	0.256

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	0.3834	0.1739	-0.7188	0.5116	-0.2893	1.7789	-0.0218	-0.0086	-0.024	-0.0251	0.0242	0.039	0.0932	0.0878	-0.0024	0.0087	0.0112	-0.0058	0.042	-0.0106	0.069	-19.0798	18.1338	27.1879
2	1.5356	0.2297	-0.2264	1.2016	-0.3106	0.4316	0.0288	0.0047	-0.0931	0.0004	-0.0125	0.0427	0.0321	-0.0193	-0.0163	0.0074	-0.004	-0.0121	0.0237	-0.0113	0.0452	1.5003	-5.2766	7.58

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	B	5 - 189
2	X-RAY DIFFRACTION	2	ALL	A	5 - 189

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