PDB-5h5v: Crystal structure of the flagellar cap protein FliD D1-D2-D3 doma...

ID or keywords:

Entry

Database: PDB / ID: 5h5v

Title

Crystal structure of the flagellar cap protein FliD D1-D2-D3 domains from Escherichia coli

Components

Flagellar hook-associated protein 2

Keywords

STRUCTURAL PROTEIN / Bacterial flagellar cap protein

Function / homology

Function and homology information

bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / extracellular region
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Song, W.S. / Cho, S.Y. / Hong, H.J. / Yoon, S.I.

Citation

Journal: J. Mol. Biol. / Year: 2017
Title: Self-Oligomerizing Structure of the Flagellar Cap Protein FliD and Its Implication in Filament Assembly.
Authors: Song, W.S. / Cho, S.Y. / Hong, H.J. / Park, S.C. / Yoon, S.I.

History

Deposition	Nov 9, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 5, 2017	Group: Database references
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h5v.cif.gz	708.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5h5v.ent.gz	594.1 KB	Display	PDB format
PDBx/mmJSON format	5h5v.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/h5/5h5v ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h5v	HTTPS FTP

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Related structure data

Related structure data	5h5tC 5h5wC 5h5s C: citing same article (ref.)
Similar structure data	0362 2r6d-d 6izq-5 6dvr-2 2r6e-1 6c58-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: Flagellar hook-associated protein 2

B: Flagellar hook-associated protein 2

C: Flagellar hook-associated protein 2

D: Flagellar hook-associated protein 2

E: Flagellar hook-associated protein 2

F: Flagellar hook-associated protein 2

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	81.062, 181.582, 110.456
Angle α, β, γ (deg.)	90.00, 105.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	104 - 223
2	1	1	1	B	104 - 223
3	1	1	1	C	104 - 223
4	1	1	1	D	104 - 223
5	1	1	1	E	104 - 223
6	1	1	1	F	104 - 223
1	1	2	1	A	72 - 103
2	1	2	1	B	72 - 103
3	1	2	1	C	72 - 103
4	1	2	1	D	72 - 103
5	1	2	1	E	72 - 103
6	1	2	1	F	72 - 103
1	2	2	1	A	224 - 267
2	2	2	1	B	224 - 267
3	2	2	1	C	224 - 267
4	2	2	1	D	224 - 267
5	2	2	1	E	224 - 267
6	2	2	1	F	224 - 267
1	1	3	1	A	46 - 71
2	1	3	1	B	46 - 71
3	1	3	1	C	46 - 71
4	1	3	1	D	46 - 71
5	1	3	1	E	46 - 71
6	1	3	1	F	46 - 71
1	1	4	1	A	268 - 416
2	1	4	1	B	268 - 416
3	1	4	1	C	268 - 416
4	1	4	1	D	268 - 416
5	1	4	1	E	268 - 416
6	1	4	1	F	268 - 416

NCS ensembles :

ID
1
2
3
4

#1: Protein	Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein Mass: 39145.250 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 43-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fliD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A094VPA5, UniProt: P24216*PLUS
Has protein modification	Y

#1: Protein

Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein

Mass: 39145.250 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 43-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: fliD / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A094VPA5, UniProt: P24216*PLUS

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: 3.34 Å³/Da / Density % sol: 63.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0-7.4, 14-18% PEG 6000 / PH range: 7.0-7.4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00005 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 25, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00005 Å / Relative weight: 1
Reflection	Resolution: 3→30 Å / Num. obs: 61902 / % possible obs: 99.9 % / Redundancy: 3.6 % / R_merge(I) obs: 0.088 / Net I/σ(I): 23.8
Reflection shell	Resolution: 3→3.05 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3→30 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.887 / Cross valid method: THROUGHOUT / ESU R: 1.626 / ESU R Free: 0.385 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25781	3105	5.1 %	RANDOM
R_work	0.22768	-	-	-
obs	0.22923	58224	99.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 72.4 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.82 Å²	0 Å²	-0.32 Å²
2-	-	6.07 Å²	0 Å²
3-	-	-	4.58 Å²

Refinement step

Cycle: 1 / Resolution: 3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13919	0	0	0	13919

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	14002
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	8101
X-RAY DIFFRACTION	r_angle_refined_deg	1.358	1.942	19151
X-RAY DIFFRACTION	r_angle_other_deg	4.819	3	20236
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.42	5	2008
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.515	27.285	453
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.85	15	2060
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.875	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	2542
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	16184
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2418
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.059	1.5	9965
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	4163
X-RAY DIFFRACTION	r_mcangle_it	0.194	2	15793
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.783	3	4037
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.306	4.5	3358
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1319	tight positional	0.04	0.05
1	1	B	1319	tight positional	0.04	0.05
1	1	C	1319	tight positional	0.04	0.05
1	1	D	1319	tight positional	0.05	0.05
1	1	E	1319	tight positional	0.04	0.05
1	1	F	1319	tight positional	0.08	0.05
2	2	A	801	tight positional	0.04	0.05
2	2	B	801	tight positional	0.04	0.05
2	2	C	801	tight positional	0.05	0.05
2	2	D	801	tight positional	0.04	0.05
2	2	E	801	tight positional	0.04	0.05
2	2	F	801	tight positional	0.04	0.05
3	3	A	153	tight positional	0.04	0.05
3	3	B	153	tight positional	0.03	0.05
3	3	C	153	tight positional	0.04	0.05
3	3	D	153	tight positional	0.03	0.05
3	3	E	153	tight positional	0.02	0.05
3	3	F	153	tight positional	0.03	0.05
4	4	A	572	tight positional	0.04	0.05
4	4	B	572	tight positional	0.03	0.05
4	4	C	572	tight positional	0.05	0.05
4	4	D	572	tight positional	0.05	0.05
4	4	E	572	tight positional	0.05	0.05
4	4	F	572	tight positional	0.03	0.05
1	1	A	1319	tight thermal	0.02	0.5
1	1	B	1319	tight thermal	0.02	0.5
1	1	C	1319	tight thermal	0.03	0.5
1	1	D	1319	tight thermal	0.03	0.5
1	1	E	1319	tight thermal	0.02	0.5
1	1	F	1319	tight thermal	0.04	0.5
2	2	A	801	tight thermal	0.02	0.5
2	2	B	801	tight thermal	0.01	0.5
2	2	C	801	tight thermal	0.02	0.5
2	2	D	801	tight thermal	0.02	0.5
2	2	E	801	tight thermal	0.02	0.5
2	2	F	801	tight thermal	0.01	0.5
3	3	A	153	tight thermal	0	0.5
3	3	B	153	tight thermal	0	0.5
3	3	C	153	tight thermal	0	0.5
3	3	D	153	tight thermal	0	0.5
3	3	E	153	tight thermal	0	0.5
3	3	F	153	tight thermal	0	0.5
4	4	A	572	tight thermal	0	0.5
4	4	B	572	tight thermal	0	0.5
4	4	C	572	tight thermal	0	0.5
4	4	D	572	tight thermal	0	0.5
4	4	E	572	tight thermal	0	0.5
4	4	F	572	tight thermal	0	0.5

LS refinement shell

Resolution: 3→3.077 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	212	-
R_work	0.338	4237	-
obs	-	-	99.84 %

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	4.2852	-1.2937	0.4047	5.2314	1.3002	3.2166	0.3107	-0.3714	0.6796	-0.4449	0.2616	-0.6155	-0.3416	0.6011	-0.5723	1.058	-0.1425	0.1754	0.1661	-0.1845	0.2411	59.582	-87.958	-7.984
2	7.0296	1.5321	-0.8139	2.3234	-0.1449	3.5251	0.2028	-0.1507	0.5638	0.0934	-0.1984	-0.0703	-0.4647	-0.2421	-0.0043	1.0175	0.0874	0.0608	0.1803	-0.1019	0.1473	22.895	-91.176	3.299
3	2.4628	-1.2097	0.4262	6.9907	-0.8227	6.5004	0.0156	-0.0609	-0.6112	0.419	-0.1995	0.277	0.7051	-0.1476	0.1839	0.9597	-0.0391	0.1052	0.3697	-0.0189	0.1739	18.095	-119.695	23.292
4	11.8503	2.797	-0.8147	5.6064	0.3805	4.5076	0.3357	-0.7123	-0.5774	0.4999	-0.9254	-1.4795	0.0065	0.8136	0.5896	1.176	-0.1013	-0.0992	0.5565	0.3676	0.9573	58.26	-50.831	-6.572
5	6.9319	1.9387	-0.468	7.5875	-1.6047	5.5535	0.2822	-0.3408	0.2374	0.2965	-0.1324	-0.0187	-0.3263	0.4537	-0.1497	0.9799	0.0584	0.1069	0.2203	-0.1547	0.2371	22.498	-62.625	-3.916
6	2.3391	-1.4745	-0.5486	6.69	1.2801	4.4712	0.1225	0.3323	0.2012	-0.7305	-0.2131	-0.0388	0.0389	-0.2778	0.0906	0.9564	0.0416	0.0037	0.2134	-0.0698	0.0772	19.923	-94.423	-18.192
7	6.8098	0.6051	-0.0052	2.0288	-0.253	1.5506	0.0623	0.1478	-0.1602	0.1629	-0.0353	-0.3474	-0.1059	0.3109	-0.0269	0.9982	0.0174	0.0299	0.1859	0.1067	0.1752	55.401	-30.693	30.513
8	5.9903	0.7031	3.0368	2.1588	1.147	5.2444	0.0612	-0.0102	-0.5163	0.06	-0.1055	0.0462	0.2863	0.0622	0.0443	0.8858	-0.0083	0.1446	0.0134	0.0247	0.2726	20.293	-41.746	17.628
9	3.4739	-1.8024	-1.8414	6.4527	0.8542	6.0061	0.5729	0.5585	0.4255	-1.6129	-0.2508	-0.221	-0.7345	-0.0992	-0.322	1.3209	0.1104	0.2003	0.2806	-0.0464	0.2837	18.748	-45.731	-17.32
10	14.9155	3.4432	0.9572	2.57	0.6306	4.8937	0.9179	-2.1156	-1.2694	0.423	-0.4742	-1.0159	-0.2578	0.9041	-0.4436	1.4704	0.1362	-0.1067	1.1813	0.3354	1.095	52.845	-50.415	60.762
11	8.4165	-0.0561	0.357	2.8549	-0.0079	7.7242	-0.083	-0.2687	-0.466	0.0441	-0.1378	-0.411	1.0058	0.3195	0.2209	1.239	0.1607	0.164	0.0482	0.0861	0.221	17.957	-49.814	45.56
12	1.7042	0.5978	-0.9149	4.1534	-0.6828	3.4506	0.1482	-0.0082	0.3315	0.1366	-0.0794	0.2006	-0.4962	-0.1064	-0.0689	0.8309	0.0609	0.1021	0.0522	-0.0069	0.1747	15.452	-21.873	24.686
13	13.4792	-6.7612	1.1381	3.4796	-0.6471	0.2293	0.0496	0.0246	-3.8226	0.1172	-0.1276	1.4385	-0.0578	0.5662	0.0781	1.2926	0.0104	0.1415	3.3944	0.3234	4.5592	54.805	-89.824	57.221
14	9.8517	4.03	0.0252	12.6775	-0.0791	6.9187	-0.1141	1.2834	-0.8525	-0.9377	0.4523	-1.3379	0.1935	0.3902	-0.3382	1.2054	0.061	0.1448	0.4025	0.024	0.2824	18.322	-78.942	52.201
15	3.8906	0.942	0.2514	6.0814	1.3854	6.7897	0.0903	-1.261	0.2666	0.4392	-0.1859	0.1021	-0.1922	-0.2921	0.0957	1.001	0.0367	0.113	0.4736	-0.0179	0.1255	12.547	-47.409	66.328
16	14.4766	1.4671	-1.3314	2.4324	-1.2482	9.9869	0.3659	-0.2862	-0.1858	-0.1131	-0.2889	-1.0808	-0.1356	1.6326	-0.077	1.3728	-0.284	0.306	1.039	-0.0063	0.8856	57.696	-109.986	26.449
17	8.6581	-0.8022	-1.1871	5.4757	3.0802	5.4449	-0.141	0.6461	0.3553	-0.8578	-0.1049	-0.1194	-0.7818	0.4314	0.2459	1.2371	-0.0904	0.0922	0.5315	0.1638	0.0804	21.19	-99.908	31.5
18	1.297	1.013	0.1121	3.8997	0.2278	6.7094	0.054	0.2431	-0.0052	0.2376	0.0796	0.0657	-0.1402	0.0391	-0.1337	0.9181	0.0411	0.0347	0.1192	0.0549	0.1183	14.607	-95.586	65.725

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	44 - 71
2	X-RAY DIFFRACTION	1	A	268 - 411
3	X-RAY DIFFRACTION	2	A	72 - 103
4	X-RAY DIFFRACTION	2	A	224 - 267
5	X-RAY DIFFRACTION	3	A	104 - 223
6	X-RAY DIFFRACTION	4	B	48 - 71
7	X-RAY DIFFRACTION	4	B	268 - 409
8	X-RAY DIFFRACTION	5	B	72 - 103
9	X-RAY DIFFRACTION	5	B	224 - 267
10	X-RAY DIFFRACTION	6	B	104 - 223
11	X-RAY DIFFRACTION	7	C	43 - 71
12	X-RAY DIFFRACTION	7	C	268 - 411
13	X-RAY DIFFRACTION	8	C	72 - 103
14	X-RAY DIFFRACTION	8	C	224 - 267
15	X-RAY DIFFRACTION	9	C	104 - 223
16	X-RAY DIFFRACTION	10	D	43 - 71
17	X-RAY DIFFRACTION	10	D	268 - 409
18	X-RAY DIFFRACTION	11	D	72 - 103
19	X-RAY DIFFRACTION	11	D	224 - 267
20	X-RAY DIFFRACTION	12	D	104 - 223
21	X-RAY DIFFRACTION	13	E	54 - 71
22	X-RAY DIFFRACTION	13	E	268 - 406
23	X-RAY DIFFRACTION	14	E	72 - 103
24	X-RAY DIFFRACTION	14	E	224 - 267
25	X-RAY DIFFRACTION	15	E	104 - 223
26	X-RAY DIFFRACTION	16	F	50 - 71
27	X-RAY DIFFRACTION	16	F	268 - 401
28	X-RAY DIFFRACTION	17	F	72 - 103
29	X-RAY DIFFRACTION	17	F	224 - 267
30	X-RAY DIFFRACTION	18	F	104 - 223

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi