PDB-8p3n: Structure of the Histidine Kinase CheA ATP-Binding domain in comp...

ID or keywords:

Entry

Database: PDB / ID: 8p3n

Title

Structure of the Histidine Kinase CheA ATP-Binding domain in complex with compound ODDHK8

Components

Chemotaxis protein CheA

Keywords

SIGNALING PROTEIN / Inhibitor / Transferase / Fragment

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: 2 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 ODDHK8
Authors: Adhav, A. / Marina, A.

History

Deposition	May 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8p3n.cif.gz	354.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8p3n.ent.gz	219.1 KB	Display	PDB format
PDBx/mmJSON format	8p3n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8p3n_validation.pdf.gz	914.3 KB	Display	wwPDB validaton report
Full document	8p3n_full_validation.pdf.gz	918.3 KB	Display
Data in XML	8p3n_validation.xml.gz	15.3 KB	Display
Data in CIF	8p3n_validation.cif.gz	20.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p3/8p3n ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p3n	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

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, Protein observed as monomer.

Unit cell

Length a, b, c (Å)	40.978, 59.021, 66.526
Angle α, β, γ (deg.)	90.000, 97.318, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
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 / Auth asym-ID: B / Label asym-ID: A / Auth seq-ID: 5 - 189 / Label seq-ID: 5 - 189

Dom-ID
1
2

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-ADZ / 9-METHYL-9H-PURIN-6-AMINE Mass: 149.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₇N₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / 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: 35.01 %
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: 2→65.98 Å / Num. obs: 21093 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.053 / R_pim(I) all: 0.033 / R_rim(I) all: 0.063 / Net I/σ(I): 20.3
Reflection shell	Resolution: 2→2.052 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.187 / Num. unique obs: 1525 / CC_1/2: 0.987 / R_pim(I) all: 0.118 / R_rim(I) all: 0.222

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→44.029 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.915 / WR_factor R_free: 0.256 / WR_factor R_work: 0.192 / SU B: 8.726 / SU ML: 0.119 / Average fsc free: 0.9602 / Average fsc work: 0.9801 / Cross valid method: FREE R-VALUE / ESU R: 0.209 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2435	1010	4.792 %
R_work	0.1848	20068	-
all	0.188	-	-
obs	-	21078	98.321 %

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: 28.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.093 Å²	0 Å²	-0.299 Å²
2-	-	-0.791 Å²	-0 Å²
3-	-	-	1.898 Å²

Refinement step

Cycle: LAST / Resolution: 2→44.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2668	0	22	75	2765

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	2722
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2692
X-RAY DIFFRACTION	r_angle_refined_deg	2.043	1.643	3660
X-RAY DIFFRACTION	r_angle_other_deg	0.66	1.576	6212
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.421	5	342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.504	5	19
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.041	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.14	10	520
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.355	10	119
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	423
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	3131
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	551
X-RAY DIFFRACTION	r_nbd_refined	0.24	0.2	532
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	2501
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1367
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1640
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	74
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.356	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.318	0.2	82
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.122	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.468	2.158	1380
X-RAY DIFFRACTION	r_mcbond_other	3.461	2.158	1380
X-RAY DIFFRACTION	r_mcangle_it	4.566	3.843	1718
X-RAY DIFFRACTION	r_mcangle_other	4.564	3.846	1719
X-RAY DIFFRACTION	r_scbond_it	5.249	2.824	1342
X-RAY DIFFRACTION	r_scbond_other	5.249	2.824	1342
X-RAY DIFFRACTION	r_scangle_it	7.935	4.87	1942
X-RAY DIFFRACTION	r_scangle_other	7.933	4.87	1943
X-RAY DIFFRACTION	r_lrange_it	9.027	26.344	2959
X-RAY DIFFRACTION	r_lrange_other	9.03	26.356	2957
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.142	0.05	4947

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	0.1418	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.1418	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
2-2.052	0.289	73	0.171	1525	0.176	1608	0.948	0.982	99.3781	0.163
2.052-2.108	0.271	84	0.186	1427	0.19	1528	0.957	0.978	98.8874	0.175
2.108-2.169	0.256	71	0.185	1398	0.188	1488	0.961	0.978	98.7231	0.175
2.169-2.236	0.286	66	0.178	1357	0.183	1434	0.952	0.98	99.2329	0.17
2.236-2.309	0.218	61	0.172	1332	0.174	1398	0.965	0.983	99.6423	0.166
2.309-2.389	0.218	67	0.164	1283	0.167	1357	0.971	0.984	99.4842	0.16
2.389-2.479	0.269	76	0.169	1242	0.175	1328	0.957	0.983	99.247	0.167
2.479-2.58	0.25	56	0.181	1194	0.184	1259	0.962	0.981	99.2851	0.178
2.58-2.695	0.323	45	0.178	1143	0.182	1203	0.935	0.981	98.7531	0.178
2.695-2.826	0.216	48	0.169	1078	0.172	1148	0.969	0.982	98.0836	0.171
2.826-2.978	0.246	62	0.182	1049	0.185	1115	0.967	0.98	99.6413	0.188
2.978-3.158	0.281	56	0.198	996	0.203	1056	0.955	0.976	99.6212	0.203
3.158-3.374	0.272	42	0.209	940	0.212	987	0.955	0.972	99.4934	0.223
3.374-3.643	0.247	42	0.2	855	0.202	902	0.957	0.976	99.4457	0.212
3.643-3.988	0.178	27	0.182	653	0.182	853	0.977	0.981	79.7186	0.2
3.988-4.454	0.21	38	0.171	729	0.173	782	0.968	0.983	98.0818	0.188
4.454-5.134	0.159	35	0.163	645	0.162	685	0.989	0.986	99.2701	0.186
5.134-6.267	0.249	26	0.238	538	0.239	573	0.975	0.974	98.4293	0.259
6.267-8.774	0.221	18	0.217	422	0.218	452	0.981	0.976	97.3451	0.251
8.774-44.029	0.392	17	0.184	262	0.196	281	0.912	0.979	99.2883	0.221

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	1.0993	-0.2109	-0.4115	0.5056	0.18	0.2607	0.0386	-0.018	-0.0479	-0.0065	-0.0346	0.0035	0.0023	-0.033	-0.004	0.0148	-0.0021	0.0011	0.0275	0.009	0.0125	14.8932	-7.0509	25.486
2	0.4233	0.3298	-0.4895	0.662	-0.8154	2.0656	-0.0286	0.0074	-0.0041	-0.015	0.0535	0.0513	0.0959	0.0398	-0.025	0.0072	0.0048	0.005	0.0355	-0.0066	0.0203	5.2462	-13.1914	-5.6384

Refinement TLS group

Selection: ALL

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