PDB-4wxm: FleQ REC domain from Pseudomonas aeruginosa PAO1

ID or keywords:

Entry

Database: PDB / ID: 4wxm

Title

FleQ REC domain from Pseudomonas aeruginosa PAO1

Components

Transcriptional regulator FleQ

Keywords

TRANSCRIPTION REGULATOR / Ntrc superfamily / Regulatory domain / C-di-GMP binding / Biofilm

Function / homology

Function and homology information

positive regulation of cilium-dependent cell motility / regulation of bacterial-type flagellum-dependent cell motility / cyclic-di-GMP binding / negative regulation of extracellular matrix assembly / positive regulation of cell-substrate adhesion / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding ...
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Su, T. / Liu, S. / Gu, L.

Funding support

China, 1items

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: The REC domain mediated dimerization is critical for FleQ from Pseudomonas aeruginosa to function as a c-di-GMP receptor and flagella gene regulator
Authors: Su, T. / Liu, S. / Wang, K. / Chi, K. / Zhu, D. / Wei, T. / Huang, Y. / Guo, L. / Hu, W. / Xu, S. / Lin, Z. / Gu, L.

History

Deposition	Nov 14, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 21, 2015	Group: Database references
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wxm.cif.gz	266.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4wxm.ent.gz	219.1 KB	Display	PDB format
PDBx/mmJSON format	4wxm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4wxm_validation.pdf.gz	464.9 KB	Display	wwPDB validaton report
Full document	4wxm_full_validation.pdf.gz	480.5 KB	Display
Data in XML	4wxm_validation.xml.gz	24.1 KB	Display
Data in CIF	4wxm_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/4wxm ftp://data.pdbj.org/pub/pdb/validation_reports/wx/4wxm	HTTPS FTP

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Related structure data

Related structure data	4wxo
Similar structure data	5c35-d 3wt2-2 1pbi-1 2r8u-d 1zkf-d 4u2u-d 3wt2-1 1k68-d 4ica-d 1whi-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4wxo

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Transcriptional regulator FleQ

B: Transcriptional regulator FleQ

C: Transcriptional regulator FleQ

D: Transcriptional regulator FleQ

E: Transcriptional regulator FleQ

81.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcriptional regulator FleQ

B: Transcriptional regulator FleQ

defined by author&software
32.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Transcriptional regulator FleQ

D: Transcriptional regulator FleQ

defined by author&software
32.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Transcriptional regulator FleQ

defined by author&software
32.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	144.397, 58.451, 92.213
Angle α, β, γ (deg.)	90.00, 118.35, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Transcriptional regulator FleQ Mass: 16273.387 Da / Num. of mol.: 5 / Fragment: REC domain, UNP residues 1-139 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: fleQ, PA1097 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XCV0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.82 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 34% PEG 4000, 0.1 M Tris-HCl, 0.2 M Sodium acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2011
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 30312 / % possible obs: 100 % / Redundancy: 3.6 % / R_merge(I) obs: 0.062 / Net I/σ(I): 33
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.397 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
SCALEPACK		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→34.071 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.271	1533	5.06 %	Random selection
R_work	0.2104	-	-	-
obs	0.2136	30293	99.23 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→34.071 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5071	0	0	32	5103

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5160
X-RAY DIFFRACTION	f_angle_d	1.274	7004
X-RAY DIFFRACTION	f_dihedral_angle_d	19.483	1961
X-RAY DIFFRACTION	f_chiral_restr	0.049	791
X-RAY DIFFRACTION	f_plane_restr	0.006	910

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 (%)
2.2954-2.3695	0.4352	138	0.3137	2511	X-RAY DIFFRACTION	96
2.3695-2.4542	0.3937	132	0.2987	2610	X-RAY DIFFRACTION	100
2.4542-2.5524	0.4097	145	0.2978	2575	X-RAY DIFFRACTION	100
2.5524-2.6685	0.334	128	0.2672	2658	X-RAY DIFFRACTION	100
2.6685-2.8091	0.3215	136	0.2709	2613	X-RAY DIFFRACTION	100
2.8091-2.985	0.3149	132	0.2681	2616	X-RAY DIFFRACTION	100
2.985-3.2153	0.3558	132	0.2589	2637	X-RAY DIFFRACTION	100
3.2153-3.5386	0.3008	157	0.229	2616	X-RAY DIFFRACTION	100
3.5386-4.0499	0.2611	151	0.2058	2611	X-RAY DIFFRACTION	100
4.0499-5.0998	0.2079	140	0.1568	2665	X-RAY DIFFRACTION	100
5.0998-34.075	0.2132	142	0.1667	2648	X-RAY DIFFRACTION	97

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	0.6473	-1.1544	0.0298	1.6672	-0.2458	0.2731	-0.2762	-0.2143	-0.7835	0.0701	0.2585	0.0854	0.6275	-0.2148	0.0007	0.5466	-0.0922	0.0055	0.6438	0.0329	0.5758	2.4706	10.39	21.849
2	0.3648	-0.4476	0.2868	0.8893	-0.0893	0.2039	-0.4222	0.0776	-0.2398	-0.0425	0.5087	0.4021	0.1534	0.1048	0.0001	0.4484	-0.1189	-0.0319	0.8426	0.1395	0.5287	-6.8318	16.7464	21.0563
3	0.1486	0.1323	0.1369	0.4381	0.0528	0.0942	-0.1481	-0.3186	0.0483	-0.1706	0.3514	0.2707	-0.0515	-0.5056	0.0003	0.4739	0.0737	-0.0544	0.8128	0.184	0.4609	-3.5823	22.8831	22.9723
4	0.05	-0.1478	0.0235	0.0393	0.034	0.0098	-0.0251	0.4467	0.6721	-0.6608	0.0139	-1.5182	0.0969	-0.8399	0.0071	0.5198	-0.0115	-0.0733	0.6026	0.12	0.7608	-2.9133	24.2849	8.9293
5	0.0569	0.1857	-0.0586	0.2084	-0.1201	0.115	-0.1971	0.0616	0.4091	-0.1688	0.3229	-0.0019	-0.8992	0.2537	-0.0003	0.5226	0.0715	-0.119	0.8407	-0.059	0.5416	-3.7514	28.2449	17.1468
6	0.1736	0.1769	0.0909	0.6627	-0.216	0.3313	-0.0905	-0.2276	-0.2087	-0.0404	0.1862	-0.1125	-0.4842	-0.2488	-0	0.5384	0.0736	-0.0508	0.602	-0.0035	0.4956	6.5485	25.2264	24.6525
7	0.0673	-0.2534	0.0834	1.7362	0.0427	-0.0024	0.4332	-1.1821	0.878	0.983	1.1033	-1.7204	-0.0117	1.7619	-0.0119	0.7055	0.2023	0.2286	0.7484	0.117	0.7007	36.9659	21.1364	13.6875
8	4.384	-0.523	0.3895	2.2422	-0.0712	2.5485	0.2679	-0.049	-0.0503	0.1741	-0.0965	0.0944	0.2105	0.189	0.0002	0.5477	0.0284	0.0479	0.3183	-0.0159	0.4388	32.4756	4.9629	19.6929
9	2.0699	-2.0811	0.1752	1.2463	0.2403	0.9345	0.0951	-0.7231	0.3535	0.0366	0.1211	-0.4835	0.0284	0.0346	-0.0003	0.3834	-0.0462	-0.1013	0.4262	-0.0195	0.5615	38.3365	37.8465	33.6421
10	3.2972	-2.2992	0.2563	1.638	-0.129	0.3057	-0.2491	0.6473	1.5027	-0.4161	0.7221	-1.5937	-0.5227	0.6671	-0.3261	0.4824	0.086	0.2272	0.7063	0.1312	0.7575	47.3212	43.4191	21.5166
11	1.2168	0.5353	-0.1297	1.5882	0.0471	0.5226	0.3504	0.8911	0.3821	-0.9722	-0.267	-0.5076	0.0637	0.2549	-0.0007	0.6567	0.0901	0.056	0.7139	-0.0528	0.6286	44.0565	31.0079	22.9571
12	0.1472	0.0956	-0.173	0.5111	-0.2431	0.4722	-0.355	-0.2784	-0.6429	-0.3429	-0.0033	0.3878	-0.1841	-0.1504	-0.0002	0.4374	0.0289	-0.0489	0.3721	-0.0222	0.5942	34.5353	23.2012	29.4258
13	-0.0232	0.0026	-0.0004	0.0108	-0.0159	0.0088	-0.773	0.054	-0.7963	-0.6697	-0.4259	0.7029	0.1587	-0.4811	0.0008	0.8035	0.1796	0.1553	1.1613	0.0846	0.6591	8.2223	37.2059	17.3383
14	1.3614	0.0807	-0.0668	1.2747	1.1412	0.7914	0.8932	0.767	0.695	-0.44	-0.2994	0.0159	-0.6644	-0.5451	0.003	0.713	0.2278	0.2168	0.6235	0.2047	0.6345	10.8077	51.3181	28.9045
15	0.3669	-0.5064	-0.4125	1.6574	0.3542	0.3373	0.2744	-0.1407	0.5345	-0.0052	-0.6423	0.2699	0.0395	-0.0732	-0.0002	0.5458	0.1058	0.0578	0.791	0.0023	0.6347	1.5246	45.6494	37.1661
16	0.8753	0.6107	-0.3271	0.5271	-0.3259	0.5328	1.1506	-0.546	0.5914	-0.0877	-1.2329	-0.1374	0.2144	-0.7747	0.0152	0.5121	0.2222	-0.1021	0.8145	-0.0847	0.5296	7.3337	36.7131	30.7184
17	0.801	-0.7814	-0.4304	0.8844	0.9506	0.8442	-0.2956	-0.2262	-0.1742	-0.111	0.0686	0.3321	-0.107	0.0731	-0.0002	0.3261	0.0112	-0.0146	0.5392	0.0875	0.4044	8.9033	32.025	-1.7446
18	1.1904	0.2031	0.6439	1.0531	0.469	0.7362	-0.7546	-0.4932	0.0536	-0.1345	1.2841	-0.2645	0.171	0.1697	0.0433	0.4341	-0.042	0.0019	0.8407	-0.0249	0.4655	17.9958	29.4258	-7.0875
19	0.3502	-0.2723	0.0652	0.1784	0.0292	0.1578	0.1226	-0.312	0.8356	0.4395	0.4172	-0.0081	-1.0132	0.2455	0.0098	0.4709	-0.0919	-0.0145	0.6203	0.0335	0.4348	19.6914	37.9289	-4.4859
20	0.0726	0.015	0.1485	0.3499	-0.0725	0.2503	-0.5428	-0.2343	-0.1996	-0.0954	0.4226	-0.1891	0.5982	0.7167	-0.0007	0.5059	0.135	-0.0099	0.858	0.0005	0.392	25.3363	27.9579	3.5448
21	0.2148	-0.1642	0.1654	0.155	-0.0127	0.156	-0.7063	-0.4894	0.2844	0.4128	0.7111	-0.3365	0.3236	0.6279	0.0046	0.4361	-0.0187	-0.005	0.6441	-0.0669	0.575	22.7758	38.7567	1.4555
22	2.2162	-0.7096	-0.336	0.7937	0.3682	0.2059	-0.0375	0.4909	-1.714	1.3352	0.1542	0.4298	1.1956	-1.2982	-0.0306	0.5668	0.2984	-0.3288	1.563	-0.0876	0.3099	21.7193	33.3465	14.2244
23	-0.0228	-0.1951	0.0242	0.6871	-0.326	0.1288	-0.3359	-1.2602	0.1035	-0.0921	0.3522	0.3744	0.0936	0.9025	0.003	0.5244	0.0321	-0.0945	0.8921	-0.0186	0.3593	24.1527	39.8403	8.9797
24	0.4716	0.3529	0.379	0.6987	0.5881	0.457	0.1281	-0.6964	0.0108	0.2977	-0.13	0.1395	-0.7277	0.3496	0.0002	0.6525	0.0112	0.029	0.7288	-0.0273	0.5576	13.7049	44.8858	2.4366

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 105 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 106 through 129 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 5 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 6 through 129 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 4 through 57 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 58 through 64 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 65 through 110 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 111 through 129 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 5 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 6 through 76 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 77 through 105 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 106 through 129 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 4 through 27 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 28 through 48 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 49 through 57 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 58 through 76 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 77 through 85 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 86 through 94 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 95 through 105 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 106 through 129 )

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