PDB-6ryk: Crystal structure of the ParB-like protein PadC

ID or keywords:

Entry

Database: PDB / ID: 6ryk

Title

Crystal structure of the ParB-like protein PadC

Components

ParB-like nuclease domain protein

Keywords

CELL CYCLE / ParABS /

cytoskeleton / bactofilin / CTP

Function / homology

ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / CYTIDINE-5'-TRIPHOSPHATE / ParB-like nuclease domain protein

Function and homology information

Biological species

Myxococcus xanthus DK 1622 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Altegoer, F. / Bange, G.

Citation

Journal: Cell / Year: 2019
Title: ParB-type DNA Segregation Proteins Are CTP-Dependent Molecular Switches.
Authors: Osorio-Valeriano, M. / Altegoer, F. / Steinchen, W. / Urban, S. / Liu, Y. / Bange, G. / Thanbichler, M.

History

Deposition	Jun 10, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 22, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 15, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ryk.cif.gz	132.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6ryk.ent.gz	101.2 KB	Display	PDB format
PDBx/mmJSON format	6ryk.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/ry/6ryk ftp://data.pdbj.org/pub/pdb/validation_reports/ry/6ryk	HTTPS FTP

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Related structure data

Similar structure data	1w2f-1 2oze-d 6cjg-d 2iew-1 4y9p-2 6r7v-d 2hv6-2 6uqx-2 4n09-2 6vp4-4 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: ParB-like nuclease domain protein

B: ParB-like nuclease domain protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	36.850, 42.440, 49.530
Angle α, β, γ (deg.)	108.54, 99.15, 89.28
Int Tables number	1
Space group name H-M	P1

#1: Protein	ParB-like nuclease domain protein Mass: 25257.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Gene: MXAN_4634 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1D3H3
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 242 / 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 grow	Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 20 % (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 1.7→46.328 Å / Num. obs: 29970 / % possible obs: 97.07 % / Redundancy: 3.5 % / CC_1/2: 0.99 / R_merge(I) obs: 0.058 / Net I/σ(I): 11.03
Reflection shell	Resolution: 1.7→1.76 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.98 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2956 / CC_1/2: 0.52 / % possible all: 96.07

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
XDS		data reduction
XSCALE		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→36.74 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.03

	R_factor	Num. reflection	% reflection
R_free	0.2265	1499	5 %
R_work	0.1851	-	-
obs	0.1872	29960	97.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.7→36.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2041	0	66	242	2349

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2159
X-RAY DIFFRACTION	f_angle_d	1.236	2930
X-RAY DIFFRACTION	f_dihedral_angle_d	11.461	1840
X-RAY DIFFRACTION	f_chiral_restr	0.054	339
X-RAY DIFFRACTION	f_plane_restr	0.007	381

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 (%)
1.7-1.7549	0.3831	135	0.3268	2558	X-RAY DIFFRACTION	96
1.7549-1.8176	0.2887	135	0.2802	2568	X-RAY DIFFRACTION	97
1.8176-1.8904	0.3152	135	0.2503	2558	X-RAY DIFFRACTION	97
1.8904-1.9764	0.2982	136	0.2329	2589	X-RAY DIFFRACTION	97
1.9764-2.0806	0.2453	136	0.2116	2585	X-RAY DIFFRACTION	97
2.0806-2.211	0.2716	136	0.2026	2578	X-RAY DIFFRACTION	97
2.211-2.3817	0.2396	136	0.1869	2591	X-RAY DIFFRACTION	97
2.3817-2.6214	0.2204	137	0.1926	2601	X-RAY DIFFRACTION	97
2.6214-3.0006	0.2325	139	0.1849	2630	X-RAY DIFFRACTION	98
3.0006-3.7802	0.2052	137	0.1709	2604	X-RAY DIFFRACTION	98
3.7802-46.3454	0.1915	137	0.1555	2599	X-RAY DIFFRACTION	98

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	9.0068	0.8104	1.0965	0.9431	0.2228	9.4079	0.0642	0.1758	0.0883	-0.5959	0.0373	-0.6511	-0.1211	1.1264	0.0873	0.3566	-0.0551	0.1102	0.3744	-0.043	0.3147	19.5236	14.25	1.9337
2	3.3204	-0.3439	1.4668	5.7374	1.465	4.1938	-0.0421	0.4788	0.4704	-0.667	-0.1569	0.3685	-0.9925	-0.3888	0.153	0.4286	0.0683	-0.0629	0.2964	0.0333	0.2511	3.2035	16.8304	-3.9316
3	1.5184	1.2834	0.4191	1.6868	0.9657	4.7095	-0.1165	-0.0118	0.2458	-0.2776	0.0374	0.0498	-0.9326	0.2461	0.1157	0.2707	-0.0059	-0.0429	0.1332	0.0101	0.2233	8.556	19.8972	8.6563
4	1.8321	0.5484	-0.8526	9.557	-3.8794	8.8239	-0.0852	1.3188	0.7106	-0.7892	-0.039	-1.1008	0.2925	0.1077	0.4684	0.5858	-0.0902	0.1918	0.5457	0.0116	0.4558	20.625	15.1548	-9.3704
5	4.0909	-0.9785	-0.604	6.7177	1.9639	4.4766	0.0112	0.1565	0.2106	-0.3112	-0.1988	0.3403	-0.9125	-0.1973	0.0956	0.3288	0.0035	-0.0518	0.1767	0.0243	0.1718	7.7856	18.7007	0.5296
6	3.8617	-0.102	1.6932	3.163	1.5293	3.2202	0.0075	0.2142	0.0677	0.0236	0.3811	-0.7819	-0.3452	0.4614	-0.3065	0.2571	-0.0987	0.0919	0.3006	0.0044	0.2131	15.1669	15.2063	2.0635
7	8.5929	0.11	-5.9451	2.2353	0.4136	4.2508	-0.2568	-0.435	-0.0034	0.1348	0.2023	0.2491	0.3701	-0.2657	0.0605	0.2027	0.0414	-0.0299	0.4004	0.0487	0.2926	4.2353	3.3227	1.2822
8	3.895	-5.4856	-1.1934	2.0021	5.693	6.6628	-0.0143	1.7212	0.1019	-0.018	-0.3824	0.5992	-0.1073	-0.64	0.2783	0.2624	-0.0385	-0.007	0.708	-0.2841	0.6096	-4.6897	7.9307	15.1965
9	4.6044	0.0804	0.7618	8.2206	4.4825	9.4705	-0.2199	0.0084	-0.1916	0.5356	-0.1662	0.9683	0.0971	-0.3876	0.248	0.1811	0.0195	0.0648	0.3246	-0.003	0.3094	-7.1755	16.0499	27.9006
10	4.8743	1.1854	-1.4069	9.676	-0.0246	2.3526	-0.055	0.5979	-0.0081	-0.0324	0.0309	0.2045	-0.6243	-0.2221	-0.0895	0.2566	0.0385	0.0063	0.3782	-0.0118	0.3218	-4.1328	23.1262	24.902
11	7.9456	-2.4261	0.3053	3.7759	2.5673	8.3235	-0.3696	-0.1954	0.1667	-0.021	0.5422	-0.2239	-0.0682	1.0351	-0.091	0.2725	0.0418	-0.0098	0.4153	0.0185	0.4084	19.8056	6.5651	19.4382
12	1.8412	0.178	-1.4543	5.4165	1.8069	2.9052	-0.2581	-0.2404	-0.7207	0.2703	-0.2295	0.3139	0.7891	-0.4515	0.3473	0.3422	-0.0619	0.1083	0.2531	0.0272	0.366	3.3847	3.6116	25.3565
13	2.6432	1.5397	-0.3521	5.7623	-4.4498	3.7427	-0.5851	0.6903	-0.4816	0.0749	0.0897	0.0008	2.1601	-0.4843	0.3917	0.6023	-0.0893	0.1085	0.2573	-0.0478	0.38	4.8265	-6.0487	9.1146
14	2.4354	0.3877	0.5475	3.3023	3.483	7.9648	-0.2585	-0.0514	-0.0746	0.1475	-0.0178	-0.0437	0.3811	0.2251	0.1759	0.1922	0.0266	-0.0094	0.1867	0.0109	0.2985	12.0897	6.5155	16.2435
15	1.4347	-2.0392	1.8736	5.0551	-4.6984	4.3812	-0.5852	-2.2425	0.3506	2.5323	0.5521	-1.8197	-0.6746	1.4278	0.3526	0.5933	-0.0108	-0.0833	0.8467	0.0265	0.4619	20.6268	5.2484	30.7223
16	3.174	1.4913	0.6345	5.6033	2.4757	2.6162	-0.0147	-0.3093	-0.3458	0.1362	-0.3255	0.061	0.8382	-0.2448	0.2377	0.3131	-0.0116	0.0646	0.1843	0.0488	0.2349	7.9506	1.75	20.9428
17	2.8701	1.3821	-1.0919	4.034	-0.9526	2.2523	-0.1446	-0.1474	-0.26	0.0044	0.2622	-0.8592	0.5518	0.3836	-0.1372	0.2323	0.0544	-0.0356	0.2199	0.0315	0.231	15.1155	5.5496	19.1736
18	3.9402	-1.2653	2.9386	3.1884	0.9484	8.0653	-0.1132	0.4728	0.2058	-0.0725	0.0334	0.0185	0.1018	0.0401	0.132	0.1577	-0.0264	0.0147	0.35	0.0399	0.3002	4.1254	17.1518	20.2785
19	6.1914	6.0252	5.3682	6.0205	4.8547	5.4501	-0.1245	-0.7414	0.0733	0.2457	-0.4796	0.7807	-0.2521	-0.2093	0.3624	0.2546	-0.0293	-0.0119	0.6461	-0.2676	0.5447	-4.77	12.6226	6.3325
20	5.2096	-2.7283	-5.3083	5.9266	0.634	6.4781	-0.0447	-0.1134	0.3893	-0.7214	-0.1327	1.2818	0.1172	-0.5117	0.147	0.2822	0.0188	-0.1753	0.5017	-0.0617	0.5367	-7.1947	4.5423	-6.2785
21	5.7458	1.6288	0.7856	3.9612	-0.572	0.7364	-0.5448	0.4751	-0.0081	-0.7392	0.0919	0.6198	1.071	0.467	0.5917	0.5868	0.0474	0.0918	0.3716	-0.0184	0.27	0.4622	0.1369	-10.7453
22	4.1236	-0.3796	-3.4462	3.0997	1.5706	3.3761	-0.3502	-1.4052	-0.5905	-0.1229	-0.5782	1.0973	1.3301	-0.0416	0.7123	0.419	0.0323	-0.003	0.5893	-0.0281	0.3781	-4.7334	-3.7551	-0.654

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 289 through 301 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 302 through 316 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 317 through 336 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 337 through 341 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 342 through 356 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 357 through 371 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 372 through 385 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 386 through 390 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 391 through 403 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 404 through 421 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 289 through 301 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 302 through 316 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 317 through 326 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 327 through 336 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 337 through 341 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 342 through 356 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 357 through 371 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 372 through 385 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 386 through 390 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 391 through 403 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 404 through 408 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 409 through 420 )

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