PDB-5x0z: Crystal structure of FliM-SpeE complex from H. pylori

ID or keywords:

Entry

Database: PDB / ID: 5x0z

Title

Crystal structure of FliM-SpeE complex from H. pylori

Components

Flagellar motor switch protein (FliM)Flagellar motor switch protein
Polyamine aminopropyltransferase

Keywords

TRANSFERASE/MOTOR PROTEIN /

flagellar motor /

H. pylori /

motility / TRANSFERASE-MOTOR PROTEIN complex

Function / homology

Function and homology information

spermidine synthase /

spermidine synthase activity / polyamine biosynthetic process / spermidine biosynthetic process / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity /

plasma membrane /

cytosol
Similarity search - Function

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Zhang, H. / Au, S.W.N.

Funding support

Hong Kong, 1items

Citation

Journal: Mol. Microbiol. / Year: 2017
Title: A putative spermidine synthase interacts with flagellar switch protein FliM and regulates motility in Helicobacter pylori
Authors: Zhang, H. / Lam, K.H. / Lam, W.W.L. / Wong, S.Y.Y. / Chan, V.S.F. / Au, S.W.N.

History

Deposition	Jan 23, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5x0z.cif.gz	583.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5x0z.ent.gz	485.2 KB	Display	PDB format
PDBx/mmJSON format	5x0z.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/x0/5x0z ftp://data.pdbj.org/pub/pdb/validation_reports/x0/5x0z	HTTPS FTP

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Related structure data

Related structure data	2cmgS 4gc8S S: Starting model for refinement
Similar structure data	1otc-d 6kxk-4 6kxk-6 2wfx-d 3ut0-4 6kxk-2 6bv5-d 1lns-d 2gzh-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) 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: Polyamine aminopropyltransferase

B: Polyamine aminopropyltransferase

C: Polyamine aminopropyltransferase

D: Polyamine aminopropyltransferase

E: Flagellar motor switch protein (FliM)

F: Flagellar motor switch protein (FliM)

hetero molecules

167 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Polyamine aminopropyltransferase

B: Polyamine aminopropyltransferase

E: Flagellar motor switch protein (FliM)

hetero molecules

defined by author
83.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Polyamine aminopropyltransferase

D: Polyamine aminopropyltransferase

F: Flagellar motor switch protein (FliM)

defined by author
83.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	184.314, 184.314, 157.083
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Polyamine aminopropyltransferase / Spermidine synthase / Putrescine aminopropyltransferase / PAPT / SPDSY Mass: 30729.744 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: speE, HP_0832 / Production host: Escherichia coli (E. coli) References: UniProt: O25503, spermine synthase, spermidine synthase
#2: Protein	Flagellar motor switch protein (FliM) / Flagellar motor switch protein Mass: 22074.736 Da / Num. of mol.: 2 / Fragment: UNP residues 43-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: HP_1031 / Production host: Escherichia coli (E. coli) / References: UniProt: O25675
#3: Chemical	ChemComp-FLC / CITRATE ANION / Citric acid Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.63 Å³/Da / Density % sol: 73.46 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: imidazole/hydrochloric acid, sodium citrate tribasic, ammonium sulfate

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→30 Å / Num. obs: 83101 / % possible obs: 99 % / Redundancy: 6.3 % / Net I/σ(I): 23.5

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Processing

Software

Name	Version	Classification
PHENIX	(DEV_2621: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2CMG, 4GC8

2cmg

4gc8

Resolution: 2.7→27.05 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.96

	R_factor	Num. reflection	% reflection
R_free	0.216	3924	4.81 %
R_work	0.177	-	-
obs	0.179	81649	98.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→27.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11498	0	13	87	11598

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	11752
X-RAY DIFFRACTION	f_angle_d	1.417	15833
X-RAY DIFFRACTION	f_dihedral_angle_d	10.724	7174
X-RAY DIFFRACTION	f_chiral_restr	0.07	1783
X-RAY DIFFRACTION	f_plane_restr	0.008	2005

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 (%)
2.6993-2.7321	0.3731	121	0.2575	2304	X-RAY DIFFRACTION	82
2.7321-2.7667	0.2935	127	0.2294	2468	X-RAY DIFFRACTION	88
2.7667-2.8031	0.2928	106	0.2218	2668	X-RAY DIFFRACTION	93
2.8031-2.8414	0.2875	137	0.217	2704	X-RAY DIFFRACTION	97
2.8414-2.882	0.2714	131	0.2284	2806	X-RAY DIFFRACTION	99
2.882-2.9249	0.2542	130	0.2201	2815	X-RAY DIFFRACTION	100
2.9249-2.9706	0.3094	157	0.2253	2764	X-RAY DIFFRACTION	100
2.9706-3.0192	0.2702	150	0.2151	2826	X-RAY DIFFRACTION	100
3.0192-3.0712	0.2798	161	0.2081	2822	X-RAY DIFFRACTION	100
3.0712-3.127	0.2426	139	0.2019	2795	X-RAY DIFFRACTION	100
3.127-3.187	0.246	148	0.1897	2812	X-RAY DIFFRACTION	100
3.187-3.252	0.2313	134	0.1821	2806	X-RAY DIFFRACTION	100
3.252-3.3226	0.2248	151	0.1972	2825	X-RAY DIFFRACTION	100
3.3226-3.3997	0.2693	137	0.1953	2801	X-RAY DIFFRACTION	100
3.3997-3.4846	0.2637	151	0.2207	2803	X-RAY DIFFRACTION	99
3.4846-3.5786	0.2071	143	0.1774	2802	X-RAY DIFFRACTION	100
3.5786-3.6836	0.2446	147	0.1987	2815	X-RAY DIFFRACTION	100
3.6836-3.8022	0.2032	150	0.1815	2787	X-RAY DIFFRACTION	100
3.8022-3.9377	0.2444	119	0.1981	2820	X-RAY DIFFRACTION	99
3.9377-4.0949	0.2152	142	0.1521	2835	X-RAY DIFFRACTION	100
4.0949-4.2806	0.1751	151	0.1422	2784	X-RAY DIFFRACTION	100
4.2806-4.5053	0.1622	134	0.1362	2856	X-RAY DIFFRACTION	100
4.5053-4.7861	0.1523	135	0.1267	2826	X-RAY DIFFRACTION	100
4.7861-5.1533	0.1582	124	0.1381	2844	X-RAY DIFFRACTION	100
5.1533-5.6676	0.2026	155	0.1614	2815	X-RAY DIFFRACTION	100
5.6676-6.4778	0.2059	142	0.1759	2839	X-RAY DIFFRACTION	100
6.4778-8.1245	0.1935	157	0.1711	2835	X-RAY DIFFRACTION	100
8.1245-27.054	0.1392	145	0.1506	2848	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	7.2264	0.045	-0.7308	2.3714	-0.5862	4.7167	-0.3216	-0.0172	-0.6662	0.7478	0.3976	0.5	0.8841	-0.021	-0.0675	0.5302	0.0504	0.0855	0.2281	0.0681	0.4668	-17.7086	127.2418	12.2662
2	4.5361	0.0064	0.7449	6.0832	2.5591	9.0761	0.0623	-0.5101	-0.977	-0.1918	0.1683	-0.334	0.2224	0.1709	-0.2604	0.5586	0.013	0.0871	0.2427	0.0828	0.5944	-19.78	133.2305	12.9736
3	3.4575	-0.2895	-0.1119	1.7996	-0.0049	2.6998	-0.1058	0.1587	-0.1157	-0.1243	-0.0453	0.6414	0.297	-0.2673	0.1491	0.3362	-0.0648	-0.045	0.1874	-0.0569	0.5246	-30.8652	141.083	-0.6531
4	4.6822	-0.1754	-0.8953	2.384	0.708	1.8797	-0.0648	0.796	-0.6687	-0.3171	-0.1773	0.5401	0.2748	-0.2201	0.1717	0.4538	-0.0562	-0.0933	0.3135	-0.1234	0.4454	-23.5093	133.2963	-13.3422
5	8.2877	-4.9555	-1.9197	2.0701	4.6721	3.0518	-0.3588	-0.3108	0.5394	1.126	0.2343	-0.1778	-0.4876	0.341	0.1579	0.5884	-0.0031	-0.0439	0.2127	0.0562	0.3316	-3.1694	127.214	9.1295
6	1.9454	-0.9888	0.4746	1.7825	-3.4285	5.6721	-0.0804	0.0007	-0.077	-0.2615	0.0402	-0.0011	-0.1293	-0.0497	0.0105	0.364	0.014	0.0354	0.1812	-0.0514	0.259	6.837	124.2252	-0.7621
7	2.3504	-0.4688	1.205	1.5193	-0.4211	2.3714	0.1439	0.7316	0.0735	-0.6258	-0.2321	-0.3662	0.126	0.5081	0.118	0.5498	0.0496	0.1803	0.4358	0.0289	0.2618	16.9997	129.6997	-12.2635
8	5.4138	-1.3755	-0.1027	2.4989	0.28	1.4824	-0.0849	0.2592	0.8035	-0.2735	-0.0265	-0.62	-0.2683	0.3015	0.0775	0.4429	-0.065	0.0639	0.2414	0.0799	0.4126	13.3674	144.9347	-5.9133
9	4.3848	-0.6803	0.0865	2.8326	0.8557	1.8565	0.0367	0.5954	0.4216	-0.398	-0.1388	-0.1526	-0.1471	0.1296	0.1135	0.4885	0.0135	0.0233	0.2855	0.1099	0.2706	0.0109	142.92	-13.114
10	6.499	2.8157	0.0359	7.4558	4.2919	5.1375	-0.2036	-0.1476	-0.3716	-0.9616	-0.0361	-0.462	0.0701	0.5851	0.3165	0.4719	0.011	-0.023	0.2791	0.1279	0.3479	-7.2836	179.0237	-4.2912
11	1.6657	1.4527	-1.3921	2.2606	-3.1204	5.8565	-0.1214	0.1503	-0.0384	0.2128	0.1565	-0.0065	0.0582	-0.1777	-0.0302	0.3604	-0.0292	-0.0862	0.1943	-0.0447	0.2955	1.5965	183.824	6.3667
12	1.2399	0.2967	-0.0674	1.3657	-0.4541	1.1522	0.1777	-0.4117	-0.0627	0.6013	-0.1761	-0.2977	-0.1494	0.4058	0.062	0.5342	-0.0592	-0.2049	0.3763	0.0025	0.316	11.5129	180.3606	18.6956
13	3.7328	0.7473	-0.201	2.0432	-0.083	1.3641	0.0748	-0.1775	-0.3501	0.3788	-0.0864	-0.2659	0.1284	0.2397	0.0368	0.5003	0.0275	-0.1141	0.2113	0.0603	0.3173	3.149	164.6913	16.0737
14	4.6525	0.9642	-2.0837	4.5513	0.7437	4.7768	-0.2202	-0.2462	0.5466	-0.8483	-0.0988	0.9649	-0.4829	0.011	0.0541	0.6231	-0.1211	-0.1102	0.3134	0.0656	0.4995	-15.1931	179.4601	-5.3004
15	4.5188	1.2027	-1.1473	2.9536	-0.1005	4.1468	-0.1116	0.6276	1.222	-0.3544	0.2338	0.1344	-0.3616	-0.2226	0.0959	0.6905	-0.0149	-0.2119	0.2855	0.0832	0.5403	-25.7236	171.5403	-10.3848
16	2.2214	0.3789	-0.4312	1.5546	-0.0314	2.865	-0.1363	0.0148	0.1016	-0.0211	-0.0635	0.669	-0.1794	-0.3015	0.147	0.3289	0.0235	-0.0454	0.178	-0.0273	0.5858	-32.8548	160.9583	4.061
17	4.5784	0.467	0.9726	2.8946	0.4256	1.9797	0.0312	-0.4345	0.5081	0.3043	-0.149	0.5297	-0.2382	-0.2893	0.0858	0.4516	0.0346	0.0678	0.2205	-0.0508	0.4235	-28.0612	170.0919	17.0184
18	2.6794	-0.7752	2.2335	1.8372	-0.5271	2.5823	-0.0135	-0.5656	0.0655	0.4924	0.2422	0.2429	0.0224	-0.4911	-0.1979	0.3705	0.0554	0.1274	0.3711	0.0178	0.2341	5.3594	114.2076	28.78
19	7.3224	4.0512	-1.4285	5.3702	-1.516	3.5325	0.029	-0.242	-0.2669	0.13	0.0764	-0.1933	-0.1793	0.1078	-0.0819	0.2518	0.0721	0.0253	0.2288	-0.0173	0.1434	10.6999	111.1595	21.4674
20	4.4158	-0.8452	0.819	2.5923	-0.0849	2.5492	-0.0735	-0.5478	-0.1237	0.2722	0.2428	0.3602	0.0295	-0.4243	-0.1741	0.3216	0.0592	0.0781	0.3521	0.094	0.2247	-1.1924	113.5074	26.5141
21	2.4344	0.2003	-1.3457	1.8312	-0.6041	2.3681	-0.0972	0.6607	-0.1876	-0.574	0.3403	0.2034	0.2686	-0.6006	-0.2254	0.4478	-0.1246	-0.1311	0.4139	0.0248	0.2528	-0.3693	192.4584	-25.9074
22	4.6668	-0.8624	-1.6368	2.6209	-0.2596	2.6989	0.06	0.3523	-0.0993	-0.2903	0.0723	0.1501	0.1781	-0.0648	-0.1422	0.3288	-0.0386	-0.0646	0.2534	-0.0097	0.1737	6.2235	192.4386	-18.2202
23	5.9912	-0.4732	2.504	4.3906	-1.8556	4.4086	0.1272	0.4008	-0.0828	-0.628	0.1672	-0.5853	0.6825	0.3987	-0.1799	0.3815	-0.0437	-0.0028	0.3006	-0.0423	0.1712	10.6095	192.9273	-17.3779
24	2.8025	0.3168	0.2242	2.5465	-0.3861	1.5323	-0.0992	0.164	-0.0594	-0.337	0.3006	0.3256	0.2443	-0.2839	-0.2023	0.3816	-0.1215	-0.082	0.3159	0.0719	0.2265	-4.0524	192.6895	-19.5318

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 29 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 30 THROUGH 47 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 48 THROUGH 129 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 130 THROUGH 262 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 1 THROUGH 16 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 17 THROUGH 67 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 68 THROUGH 129 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 130 THROUGH 189 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 190 THROUGH 262 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 1 THROUGH 16 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 17 THROUGH 67 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 68 THROUGH 129 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 130 THROUGH 262 )
14	X-RAY DIFFRACTION	14	CHAIN 'D' AND (RESID 1 THROUGH 16 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 17 THROUGH 47 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 48 THROUGH 129 )
17	X-RAY DIFFRACTION	17	CHAIN 'D' AND (RESID 130 THROUGH 262 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 47 THROUGH 133 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 134 THROUGH 183 )
20	X-RAY DIFFRACTION	20	CHAIN 'E' AND (RESID 184 THROUGH 237 )
21	X-RAY DIFFRACTION	21	CHAIN 'F' AND (RESID 48 THROUGH 108 )
22	X-RAY DIFFRACTION	22	CHAIN 'F' AND (RESID 109 THROUGH 133 )
23	X-RAY DIFFRACTION	23	CHAIN 'F' AND (RESID 134 THROUGH 169 )
24	X-RAY DIFFRACTION	24	CHAIN 'F' AND (RESID 170 THROUGH 230 )

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