PDB-8p6f: Crystal structure of PorX-Fj

ID or keywords:

Entry

Database: PDB / ID: 8p6f

Title

Crystal structure of PorX-Fj

Components

Response regulator receiver domain-containing protein

Keywords

UNKNOWN FUNCTION / Type IX secretion system / Flavobacterium johnsoniae /

two-component system /

response regulator

Function / homology

Function and homology information

phosphorelay signal transduction system
Similarity search - Function

Biological species

Flavobacterium johnsoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Leone, P.

Funding support

France, 1items

Citation

Journal: Sci Rep / Year: 2024
Title: Structure-function analysis of PorX Fj , the PorX homolog from Flavobacterium johnsioniae, suggests a role of the CheY-like domain in type IX secretion motor activity.
Authors: Zammit, M. / Bartoli, J. / Kellenberger, C. / Melani, P. / Roussel, A. / Cascales, E. / Leone, P.

History

Deposition	May 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 3, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p6f.cif.gz	444.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8p6f.ent.gz	358.5 KB	Display	PDB format
PDBx/mmJSON format	8p6f.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/p6/8p6f ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p6f	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 (6) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Response regulator receiver domain-containing protein

B: Response regulator receiver domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	84.609, 97.483, 131.103
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Response regulator receiver domain-containing protein Mass: 62855.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flavobacterium johnsoniae (bacteria) / Gene: SAMN05444388_11078 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M5SPD1
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.15 Å³/Da / Density % sol: 42.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Calcium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 18% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 2→40 Å / Num. obs: 73936 / % possible obs: 100 % / Redundancy: 6.7 % / CC_1/2: 0.998 / Net I/σ(I): 8.1
Reflection shell	Resolution: 2→2.11 Å / Num. unique obs: 10652 / CC_1/2: 0.319

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Processing

Software

Name	Classification
autoBUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→29.16 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.94 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU R_free Blow DPI: 0.178 / SU R_free Cruickshank DPI: 0.178

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2549	3744	5.07 %	RANDOM
R_work	0.2156	-	-	-
obs	0.2176	73840	100 %	-

Displacement parameters

B_iso mean: 53.86 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.0637 Å²	0 Å²	0 Å²
2-	-	-5.3849 Å²	0 Å²
3-	-	-	0.3213 Å²

Refine analyze

Luzzati coordinate error obs: 0.3 Å

Refinement step

Cycle: LAST / Resolution: 2→29.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8398	0	30	560	8988

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	8598	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.98	11604	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3080	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		1433	HARMONIC	5
X-RAY DIFFRACTION	t_it		8598	HARMONIC	10
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.35
X-RAY DIFFRACTION	t_other_torsion	18.29
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1106	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		7404	SEMIHARMONIC	4

LS refinement shell

Resolution: 2→2.01 Å / Total num. of bins used: 51

	R_factor	Num. reflection	% reflection
R_free	0.392	-	5.48 %
R_work	0.3949	1396	-
all	0.3948	1477	-
obs	-	-	99.87 %

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	5.2053	-0.1233	-1.394	10.0471	0.3232	6.6226	0.1152	-0.0533	0.1975	0.5438	0.0235	0.3828	-0.5466	0.0017	-0.1387	0.0341	-0.0202	0.1066	-0.1186	-0.0273	-0.1902	-15.2083	8.3316	60.8308
2	5.5638	-1.837	-1.3515	13.518	-0.2882	6.3529	-0.0081	0.1829	-0.3318	0.4681	-0.2562	1.3678	0.2435	-0.6183	0.2642	-0.0348	-0.0612	0.1387	-0.051	-0.0984	-0.0625	-19.8924	-1.4185	55.6991
3	9.1274	-2.4154	6.8011	10.9994	0.9842	18.7413	0.0615	-0.0546	-0.6179	-0.2978	0.0632	0.7669	0.6844	-0.4783	-0.1247	-0.0587	-0.0556	0.1148	-0.1327	-0.0591	-0.0421	-16.9099	-7.9816	52.4218
4	1.6804	-2.5442	-5.2816	6.8219	1.9064	0.3386	0.1182	-0.0956	0.0978	0.2144	-0.0273	0.02	0.3795	0.1929	-0.091	0.0403	-0.0497	0.0645	-0.0942	0.0098	-0.1685	-9.2378	-0.6212	52.52
5	5.521	3.0053	-3.5959	9.0598	2.8013	5.5621	-0.0569	-0.2891	-0.619	0.6094	-0.0837	-0.0621	-0.0145	0.2668	0.1406	0.0382	-0.0202	0.0456	-0.066	-0.0168	-0.0885	-3.8824	-6.4716	48.4319
6	0	1.7243	-2.2673	0	2.9249	7.1598	-0.0454	-0.5197	0.0598	1.0308	0.1405	-0.12	-0.2325	0.0956	-0.0952	0.162	-0.1109	0.0104	-0.0247	-0.019	-0.1646	-3.6772	7.1857	56.0554
7	1.7565	3.4542	-5.3053	12.6069	-12.8033	19.7233	0.1214	0.0694	0.0031	0.5022	0.1483	0.4005	-0.1694	-0.2105	-0.2697	0.0283	0.0489	0.0391	-0.0419	-0.0241	-0.1185	-10.7184	15.1448	42.4772
8	14.7806	3.5539	-12.2255	5.1918	-5.1614	13.0156	0.1641	0.3892	0.8997	0.1814	0.4428	0.4183	-0.3468	-0.4496	-0.6069	0.0026	-0.0374	-0.0236	-0.1337	-0.0175	-0.1036	-1.3891	28.959	25.3064
9	4.7289	0.0745	-7.7984	0.4704	1.263	13.5147	0.1679	-0.1259	0.4488	0.1769	0.3791	-0.2475	0.0747	0.4274	-0.5469	-0.041	-0.0313	-0.0685	-0.0389	-0.0302	-0.0287	2.6871	20.1064	19.3834
10	16.5877	3.5442	-4.8931	23.4435	-3.8681	10.9744	-0.3314	-0.2085	-0.6389	0.5252	0.536	2.1496	0.5141	-2.0024	-0.2046	-0.1214	0.0076	-0.0216	0.1995	0.0523	0.124	-12.0739	23.6258	23.671
11	7.698	-1.7337	-2.2244	5.4701	1.3984	4.9682	0.1796	-0.0047	1.156	-0.4559	0.2276	-0.654	-0.7238	0.6572	-0.4072	-0.0428	-0.2087	-0.0044	0.0495	0.0451	-0.079	7.7942	22.2813	4.4585
12	0.0131	-1.3827	0.1141	4.6346	-0.8203	0.3587	-0.0829	0.3011	-0.0868	-0.1949	-0.105	-0.6974	-0.0604	0.6577	0.1879	-0.1627	-0.0437	0.0062	0.0931	-0.0332	0.0742	15.4912	3.046	9.3761
13	1.5582	0.0734	-0.0802	2.0231	-0.6086	0.6309	-0.0806	0.1183	-0.0743	-0.3332	0.0432	-0.1618	0.0112	0.1732	0.0375	-0.0896	-0.0409	0.0157	0.0256	-0.0368	-0.0578	4.8088	1.7561	5.7572
14	6.701	1.7201	0.2304	3.3943	-0.6145	0.6017	-0.1354	0.6569	-1.256	-0.3507	-0.0377	-0.4019	0.3372	0.0427	0.1731	-0.0607	0.0428	0.0573	0.0014	-0.0876	-0.0522	5.7046	-9.9462	6.402
15	5.1297	-3.6074	1.6443	5.207	-1.1765	1.7078	-0.0316	0.2103	-0.5215	-0.1725	0.1141	0.2049	0.0947	0.043	-0.0825	-0.0534	-0.0532	0.0059	-0.02	-0.0248	-0.0742	-4.1989	-5.5578	10.4116
16	3.7018	-2.4795	0.7628	3.6364	-1.439	1.3475	-0.0358	-0.0984	0.0163	0.1681	0.0688	0.085	-0.1096	0.0159	-0.0331	-0.1108	-0.0372	-0.0079	0.0141	0.0007	-0.0255	-12.5488	3.9185	17.6783
17	2.2859	-2.1904	1.5236	4.9411	-2.2167	1.8835	0.0306	0.1501	-0.1771	-0.3919	-0.0365	-0.0325	0.1033	0.1908	0.0059	-0.0939	-0.0426	-0.0268	0.0157	-0.0194	-0.0701	-2.1224	3.5972	10.3733
18	13.022	-2.6908	0.7261	8.219	-1.6706	10.0427	0.2957	1.4698	-0.5366	-1.489	-0.7332	-0.1744	0.0313	0.0716	0.4375	0.1968	0.0424	-0.0894	0.04	-0.0174	-0.2209	-5.7447	16.787	-8.7731
19	9.2613	-1.7355	-0.1678	1.7581	-0.3651	1.2658	0.1208	1.3033	0.1616	-0.7033	-0.1414	0.0019	-0.3382	0.1856	0.0206	0.2148	-0.1191	-0.0348	0.0905	0.0776	-0.1985	-1.7171	18.6686	-7.5421
20	1.9757	-0.674	1.4277	2.9215	-1.333	2.0686	-0.0945	-0.1543	0.099	-0.2885	0.0852	0.0229	-0.0669	0.0488	0.0093	-0.0589	-0.0417	-0.015	-0.0262	-0.0139	-0.1073	-6.3346	11.3379	7.5281
21	4.7341	1.2116	0.1471	9.0142	-2.4739	5.7421	-0.0432	-0.42	-0.7078	0.379	-0.076	-0.8449	-0.1932	0.6936	0.1192	-0.1762	-0.0398	-0.055	0.0518	0.0817	-0.0108	15.0891	5.6245	46.5218
22	4.5553	0.5869	-0.5758	9.4279	-1.6526	5.256	-0.1215	0.2022	-0.1787	0.0782	-0.0236	-0.2854	-0.121	0.3511	0.1451	-0.1228	-0.1065	-0.0223	-0.0014	0.0223	-0.1667	12.255	12.2343	39.1601
23	0.5989	1.2758	-1.6063	0	-2.354	9.4516	-0.0082	0.1303	0.2186	0.1417	-0.1915	0.1698	-0.4336	-0.3264	0.1997	0.0439	-0.0734	-0.0746	0.0532	0.0179	-0.0834	4.8981	12.6751	38.6386
24	10.2339	-3.1509	-3.0359	5.3724	0.1513	10.5141	0.4154	-0.3996	0.8306	1.1493	-0.5673	0.3356	-0.8892	0.3731	0.1519	0.1688	-0.1113	0.0452	-0.1411	-0.0368	-0.0099	-2.5945	20.8031	50.8192
25	10.6389	-8.3472	0.6958	18.5623	2.8146	6.1966	0.2116	0.4379	0.3433	-0.1698	-0.204	0.0147	-0.0188	0.2786	-0.0076	0.0008	-0.0804	0.0205	-0.0185	0.0471	-0.1212	-3.0357	15.1919	41.5022
26	1.9353	1.9426	-1.1316	10.7736	3.2083	5.3693	-0.0069	-0.1476	-0.3217	0.2876	0.0162	-0.3481	-0.3749	0.529	-0.0092	-0.0444	-0.051	-0.0336	0.0091	0.0469	-0.0999	3.6449	4.0509	49.1249
27	15.9205	12.4144	2.2558	10.4565	0.4499	2.8574	0.3533	-0.4325	-0.0959	0.2769	-0.1097	-0.0541	0.2144	-0.0011	-0.2436	0.005	0.0577	0.0145	-0.0218	-0.0014	-0.1079	-13.2888	-16.26	40.2948
28	8.1758	1.4647	2.7456	0.0027	0.0109	1.7936	0.0135	-0.8339	-0.3983	0.1736	0.0224	-0.1671	0.2697	-0.4181	-0.0358	0.0417	0.0257	0.0163	0.0534	0.0588	-0.073	-29.8622	-14.3454	37.5332
29	10.0736	-1.4128	1.9223	2.1674	0.1537	2.0251	0.218	0.0708	-0.6894	0.1153	-0.0395	0.2876	0.3154	-0.1622	-0.1785	-0.0456	-0.0624	0.0384	-0.0585	0.0618	-0.1612	-31.9712	-17.5239	31.1949
30	1.8361	2.0933	-0.1775	1.5166	3.0468	6.9301	0.0047	-0.0334	0.3228	0.9584	-0.1439	1.1476	0.1192	-0.7771	0.1392	-0.1435	0.0755	0.1265	0.0598	-0.0359	0.1027	-46.491	3.7908	34.2231
31	3.3761	1.2587	-0.3435	1.9093	-0.6864	1.057	0.0402	-0.1526	0.1795	0.3227	0.0171	0.3478	-0.1402	-0.1184	-0.0573	-0.127	0.0609	0.0413	0.0416	-0.0038	-0.0054	-35.812	0.8804	28.6314
32	1.2637	0.055	3.6141	4.9298	0.2751	0.2083	0.1364	-0.1951	0.3278	-0.1476	-0.2345	0.8966	-0.3532	-0.4419	0.0981	-0.2767	0.0151	-0.0769	0.1814	0.047	0.184	-53.2629	-2.6763	14.1455
33	6.0041	-1.55	-2.0059	8.3249	4.0166	10.8531	-0.023	1.0242	0.7156	-0.4991	-0.1072	1.1166	-0.4989	-0.9978	0.1303	-0.3737	0.0292	-0.0737	0.0718	0.1059	0.295	-49.5549	4.6925	18.3516
34	6.5591	-0.5383	-1.9384	6.2592	0.2955	3.1466	-0.047	0.4769	1.0029	-0.1821	0.0646	0.8262	-0.3938	-0.1565	-0.0176	-0.1913	0.0786	-0.0461	-0.0835	0.0746	0.206	-37.2574	14.7491	21.7281
35	4.8076	-2.3594	-2.2076	8.3455	4.1841	8.3704	-0.014	0.6701	0.401	-0.5168	-0.0762	0.0602	-0.0386	-0.5174	0.0902	-0.099	0.0003	-0.0337	0.046	0.0248	-0.043	-24.0731	-4.0752	11.9151
36	2.6888	-0.8676	-1.0142	1.2093	1.1554	0	-0.0514	-0.1296	-0.0156	0.2047	-0.0817	0.1143	-0.1091	0.1504	0.1331	-0.0734	0.0182	-0.0055	0.0627	0.0118	-0.0302	-19.9548	0.2574	21.6068
37	2.5234	0.5749	-0.4947	7.3994	2.1506	1.6228	0.023	0.0601	0.3496	0.1634	0.0363	0.2629	0.0265	-0.0833	-0.0594	-0.1743	0.054	-0.0305	0.0113	0.0398	-0.0909	-32.0338	0.1148	23.7932
38	13.5491	0.5014	0.5564	11.8324	-3.3031	5.8797	-0.2288	1.6131	-0.7537	-1.4723	-0.0875	0.8006	0.6707	-0.9063	0.3163	-0.1316	-0.1094	-0.0174	0.1694	-0.2362	-0.0069	-40.9075	-21.1281	13.5946
39	5.0291	-1.8965	-5.4998	4.2444	1.5061	4.2046	-0.367	1.3548	-0.6076	-0.5549	-0.057	0.7034	0.4419	-1.0973	0.424	-0.1127	-0.1368	-0.0905	0.1857	-0.0789	0.0835	-40.9641	-19.2727	12.7915
40	1.8942	0.1241	-1.012	2.1899	1.4248	5.4872	-0.0034	-0.0759	-0.0114	0.1069	0.003	0.2135	0.0628	-0.0116	0.0003	-0.1791	-0.0044	-0.0072	0.0126	0.0221	-0.0651	-31.2394	-6.2455	24.5787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|2 - 34 }
2	X-RAY DIFFRACTION	2	{ A\|35 - 56 }
3	X-RAY DIFFRACTION	3	{ A\|57 - 73 }
4	X-RAY DIFFRACTION	4	{ A\|74 - 85 }
5	X-RAY DIFFRACTION	5	{ A\|86 - 100 }
6	X-RAY DIFFRACTION	6	{ A\|101 - 113 }
7	X-RAY DIFFRACTION	7	{ A\|114 - 128 }
8	X-RAY DIFFRACTION	8	{ A\|129 - 147 }
9	X-RAY DIFFRACTION	9	{ A\|148 - 167 }
10	X-RAY DIFFRACTION	10	{ A\|168 - 182 }
11	X-RAY DIFFRACTION	11	{ A\|183 - 208 }
12	X-RAY DIFFRACTION	12	{ A\|209 - 226 }
13	X-RAY DIFFRACTION	13	{ A\|227 - 314 }
14	X-RAY DIFFRACTION	14	{ A\|315 - 339 }
15	X-RAY DIFFRACTION	15	{ A\|340 - 370 }
16	X-RAY DIFFRACTION	16	{ A\|371 - 396 }
17	X-RAY DIFFRACTION	17	{ A\|397 - 429 }
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