PDB-5xll: Dimer form of M. tuberculosis PknI sensor domain

ID or keywords:

Entry

Database: PDB / ID: 5xll

Title

Dimer form of M. tuberculosis PknI sensor domain

Components

Serine/threonine-protein kinase PknI

Keywords

TRANSFERASE / dimer / sensor domain / PknI / M. tuberculosis

Function / homology

Function and homology information

regulation of growth rate / manganese ion binding / protein kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.201 Å

Authors

Rao, Z. / Yan, Q.

Funding support

China, 3items

Organization	Grant number	Country
Ministry of Science and Technology	2014CB542800	China
National Natural Science Foundation of China (NSFC)	81330036	China
National Natural Science Foundation of China (NSFC)	81520108019	China

Citation

Journal: Structure / Year: 2017
Title: Structural Insight into the Activation of PknI Kinase from M. tuberculosis via Dimerization of the Extracellular Sensor Domain.
Authors: Yan, Q. / Jiang, D. / Qian, L. / Zhang, Q. / Zhang, W. / Zhou, W. / Mi, K. / Guddat, L. / Yang, H. / Rao, Z.

History

Deposition	May 10, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 27, 2021	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Nov 6, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xll.cif.gz	137.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5xll.ent.gz	109.4 KB	Display	PDB format
PDBx/mmJSON format	5xll.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5xll_validation.pdf.gz	437.5 KB	Display	wwPDB validaton report
Full document	5xll_full_validation.pdf.gz	441.4 KB	Display
Data in XML	5xll_validation.xml.gz	13.8 KB	Display
Data in CIF	5xll_validation.cif.gz	18.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xl/5xll ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xll	HTTPS FTP

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Related structure data

Related structure data	5xkaC 5xlmC C: citing same article (ref.)
Similar structure data	6w7d-d 6cq6-d 6w7c-d 5eqj-d 6w83-d 6v36-d 6w88-d 6w84-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Serine/threonine-protein kinase PknI

B: Serine/threonine-protein kinase PknI

39.6 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

Unit cell

Length a, b, c (Å)	136.014, 136.014, 136.014
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

#1: Protein	Serine/threonine-protein kinase PknI Mass: 19816.605 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 402-585 Source method: isolated from a genetically manipulated source Details: selenomethionine substituted protein Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pknI, Rv2914c, MTCY338.02c / Production host: Escherichia coli (E. coli) References: UniProt: P9WI69, non-specific serine/threonine protein kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.66 Å³/Da / Density % sol: 53.83 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.1 M sodium malonate, 0.1M HEPES, 0.5% v/v Jeffamine ED-2001, pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 21387 / % possible obs: 100 % / Redundancy: 10.8 % / R_merge(I) obs: 0.093 / R_rim(I) all: 0.03 / Net I/σ(I): 55.1
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 11.2 % / R_merge(I) obs: 0.824 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1450 / CC_1/2: 0.87 / R_pim(I) all: 0.258 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.7.3_928	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.201→48.088 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.01
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns

	R_factor	Num. reflection	% reflection
R_free	0.2566	1047	9.36 %
R_work	0.2235	-	-
obs	0.2269	21387	99.96 %

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / B_sol: 40.254 Å² / k_sol: 0.355 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 2.201→48.088 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2408	0	0	59	2467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2481
X-RAY DIFFRACTION	f_angle_d	1.253	3410
X-RAY DIFFRACTION	f_dihedral_angle_d	14.651	920
X-RAY DIFFRACTION	f_chiral_restr	0.069	387
X-RAY DIFFRACTION	f_plane_restr	0.006	459

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2007-2.2275	0.3124	140	0.301	1374	X-RAY DIFFRACTION	100
2.2275-2.2557	0.2905	148	0.2752	1350	X-RAY DIFFRACTION	100
2.2557-2.2854	0.3707	126	0.3131	1286	X-RAY DIFFRACTION	100
2.2854-2.3167	0.3502	140	0.2872	1353	X-RAY DIFFRACTION	1.01
2.3167-2.3498	0.3753	136	0.2684	1336	X-RAY DIFFRACTION	100
2.3498-2.3848	0.2901	140	0.2914	1364	X-RAY DIFFRACTION	1.01
2.3848-2.4221	0.3287	146	0.2658	1307	X-RAY DIFFRACTION	100
2.4221-2.4618	0.4425	136	0.2918	1321	X-RAY DIFFRACTION	100
2.4618-2.5043	0.2815	144	0.3098	1395	X-RAY DIFFRACTION	100
2.5043-2.5498	0.3815	136	0.3033	1312	X-RAY DIFFRACTION	100
2.5498-2.5988	0.3186	130	0.2865	1325	X-RAY DIFFRACTION	100
2.5988-2.6519	0.2536	132	0.2636	1306	X-RAY DIFFRACTION	100
2.6519-2.7095	0.3544	146	0.2621	1351	X-RAY DIFFRACTION	1.01
2.7095-2.7726	0.3795	142	0.2877	1306	X-RAY DIFFRACTION	100
2.7726-2.8419	0.3936	134	0.2692	1368	X-RAY DIFFRACTION	100
2.8419-2.9187	0.3129	130	0.2413	1343	X-RAY DIFFRACTION	100
2.9187-3.0046	0.2267	138	0.2514	1358	X-RAY DIFFRACTION	100
3.0046-3.1016	0.3432	128	0.2235	1330	X-RAY DIFFRACTION	100
3.1016-3.2124	0.2819	135	0.2472	1325	X-RAY DIFFRACTION	100
3.2124-3.341	0.3016	140	0.2584	1326	X-RAY DIFFRACTION	100
3.341-3.493	0.3056	130	0.2175	1338	X-RAY DIFFRACTION	100
3.493-3.6771	0.2604	140	0.2281	1344	X-RAY DIFFRACTION	100
3.6771-3.9074	0.2357	142	0.2064	1331	X-RAY DIFFRACTION	100
3.9074-4.2089	0.1693	139	0.1792	1336	X-RAY DIFFRACTION	100
4.2089-4.6321	0.1653	144	0.1652	1323	X-RAY DIFFRACTION	100
4.6321-5.3017	0.2373	130	0.1643	1338	X-RAY DIFFRACTION	100
5.3017-6.6767	0.2117	149	0.2258	1324	X-RAY DIFFRACTION	100
6.6767-48.0997	0.2293	142	0.21	1340	X-RAY DIFFRACTION	99

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	0.6407	-0.2895	0.4696	0.6608	0.5087	0.8737	0.1901	-0.1207	-0.0251	0.2832	0.0981	-0.233	0.1408	0.0717	0	0.3481	-0.0334	-0.0556	0.314	-0.0307	0.4462	91.7312	30.0536	3.0108
2	1.5673	-0.6356	1.3595	1.0505	-0.1366	1.3377	-0.1404	0.1548	0.1762	0.0317	0.3229	-0.0565	-0.2737	-0.4073	0.0204	0.4321	0.0774	-0.1016	0.2998	0.0538	0.3667	62.6118	43.9608	23.5022
3	1.9385	-0.8633	0.2944	2.0065	1.2233	1.1697	-0.074	0.2708	0.0626	-0.5605	-0.2803	-0.4361	-0.1176	0.0171	-0	0.3893	0.1505	-0.0313	0.3937	0.0402	0.3515	57.4528	48.3922	18.0296
4	1.096	-1.0817	-0.4917	0.8358	0.3475	0.664	0.1097	-0.1265	-0.5995	0.1932	-0.0464	0.5	-0.3592	-0.415	0.0123	0.3569	0.0128	-0.1048	0.4517	0.061	0.5937	59.325	34.6527	22.4095
5	0.3619	0.3436	-0.2452	0.5496	0.0294	0.2434	-0.1456	0.8624	-0.2863	-0.0975	-0.4214	0.1259	-0.3134	-0.4141	-0.0162	0.3458	0.0684	-0.1185	0.6835	-0.0247	0.688	70.8553	26.8603	7.9407
6	1.5089	-0.187	-0.1093	0.3336	-0.0684	0.0423	-0.0047	-1.0428	-0.4621	0.2561	-0.2466	-0.1001	-0.8361	0.4567	-0.0227	0.5148	-0.0453	-0.1117	0.4806	0.0337	0.3861	68.4502	40.8699	30.8792
7	1.6859	-0.6104	1.1103	0.471	-0.0881	2.5684	-0.2587	-0.1296	-0.4308	0.187	0.2714	0.0679	-0.0001	-0.0462	-0.0162	0.2593	-0.0353	-0.0136	0.2606	0.04	0.459	63.8019	36.7347	20.0149
8	0.3678	-0.3089	0.0314	0.9063	0.4983	0.3326	0.0878	-0.0036	0.203	-0.1242	-0.2663	0.135	-0.3284	-0.2397	-0.0303	0.3494	0.0832	0.0297	0.4207	-0.0438	0.3405	43.9739	3.0138	30.5511
9	4.4422	0.0897	1.585	1.5038	0.8717	0.9837	-0.1289	0.271	-0.0314	0.0873	0.1032	-0.3029	0.0819	-0.072	0	0.3644	0.0717	-0.0572	0.3742	0.0375	0.3457	76.915	22.482	42.9562
10	3.8677	1.6239	0.7372	1.0265	0.6807	1.239	-0.0165	-0.5929	-1.9414	-0.0491	0.4331	-0.6297	0.3221	0.062	0.0292	0.3496	0.1548	-0.0191	0.7365	-0.0174	0.6875	66.7956	7.3936	26.7046
11	1.452	0.5226	0.1993	0.5232	-0.2808	0.4378	0.0849	0.6796	0.5795	0.4414	-0.0207	0.0951	-0.1141	0.1585	0.0001	0.4043	0.0837	0.0096	0.408	0.0494	0.3877	68.3163	28.3535	38.6347
12	1.1379	-0.4297	0.0462	2.2252	0.3661	0.075	-0.1548	0.3535	0.098	0.1088	0.0248	-0.0602	0.0281	-0.0389	-0.0014	0.3241	0.0382	-0.0008	0.4689	0.0195	0.3014	72.6718	20.0257	36.6954

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 403:427)
2	X-RAY DIFFRACTION	2	(chain A and resid 428:446)
3	X-RAY DIFFRACTION	3	(chain A and resid 447:466)
4	X-RAY DIFFRACTION	4	(chain A and resid 467:489)
5	X-RAY DIFFRACTION	5	(chain A and resid 490:507)
6	X-RAY DIFFRACTION	6	(chain A and resid 508:521)
7	X-RAY DIFFRACTION	7	(chain A and resid 522:560)
8	X-RAY DIFFRACTION	8	(chain B and resid 402:428)
9	X-RAY DIFFRACTION	9	(chain B and resid 429:483)
10	X-RAY DIFFRACTION	10	(chain B and resid 484:504)
11	X-RAY DIFFRACTION	11	(chain B and resid 505:521)
12	X-RAY DIFFRACTION	12	(chain B and resid 522:561)

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