PDB-5h5t: Crystal structure of the flagellar cap protein FliD D2-D3 domains...

ID or keywords:

Entry

Database: PDB / ID: 5h5t

Title

Crystal structure of the flagellar cap protein FliD D2-D3 domains from Salmonella Typhimurium

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

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 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 8, 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 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h5t.cif.gz	363.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5h5t.ent.gz	299.4 KB	Display	PDB format
PDBx/mmJSON format	5h5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5h5t_validation.pdf.gz	463 KB	Display	wwPDB validaton report
Full document	5h5t_full_validation.pdf.gz	473.2 KB	Display
Data in XML	5h5t_validation.xml.gz	34.5 KB	Display
Data in CIF	5h5t_validation.cif.gz	47.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h5/5h5t ftp://data.pdbj.org/pub/pdb/validation_reports/h5/5h5t	HTTPS FTP

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Related structure data

Related structure data	5h5vSC 5h5wC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5vpe-d 5vpf-d 3v58-2 3v57-2 6xwk-1 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

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	78.688, 106.062, 141.704
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
1	2	A
2	2	B
3	2	C
4	2	D
5	2	E

NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	THR	THR	A	A	76 - 87	12 - 23
2	1	1	SER	SER	THR	THR	B	B	76 - 87	12 - 23
3	1	1	SER	SER	THR	THR	C	C	76 - 87	12 - 23
4	1	1	SER	SER	THR	THR	D	D	76 - 87	12 - 23
5	1	1	SER	SER	THR	THR	E	E	76 - 87	12 - 23
1	2	1	ASN	ASN	THR	THR	A	A	226 - 264	162 - 200
2	2	1	ASN	ASN	THR	THR	B	B	226 - 264	162 - 200
3	2	1	ASN	ASN	THR	THR	C	C	226 - 264	162 - 200
4	2	1	ASN	ASN	THR	THR	D	D	226 - 264	162 - 200
5	2	1	ASN	ASN	THR	THR	E	E	226 - 264	162 - 200
1	3	1	ALA	ALA	ALA	ALA	A	A	90 - 103	26 - 39
2	3	1	ALA	ALA	ALA	ALA	B	B	90 - 103	26 - 39
3	3	1	ALA	ALA	ALA	ALA	C	C	90 - 103	26 - 39
4	3	1	ALA	ALA	ALA	ALA	D	D	90 - 103	26 - 39
5	3	1	ALA	ALA	ALA	ALA	E	E	90 - 103	26 - 39
1	1	2	ALA	ALA	LYS	LYS	A	A	104 - 145	40 - 81
2	1	2	ALA	ALA	LYS	LYS	B	B	104 - 145	40 - 81
3	1	2	ALA	ALA	LYS	LYS	C	C	104 - 145	40 - 81
4	1	2	ALA	ALA	LYS	LYS	D	D	104 - 145	40 - 81
5	1	2	ALA	ALA	LYS	LYS	E	E	104 - 145	40 - 81
1	2	2	SER	SER	GLU	GLU	A	A	152 - 225	88 - 161
2	2	2	SER	SER	GLU	GLU	B	B	152 - 225	88 - 161
3	2	2	SER	SER	GLU	GLU	C	C	152 - 225	88 - 161
4	2	2	SER	SER	GLU	GLU	D	D	152 - 225	88 - 161
5	2	2	SER	SER	GLU	GLU	E	E	152 - 225	88 - 161

NCS ensembles :

ID
1
2

#1: Protein	Flagellar hook-associated protein 2 / HAP2 / Flagellar cap protein Mass: 21535.938 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 71-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: fliD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6FM27, UniProt: P16328*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

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

Mass: 21535.938 Da / Num. of mol.: 5 / Fragment: UNP RESIDUES 71-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella typhimurium (bacteria) / Gene: fliD / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6FM27, UniProt: P16328*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.75 Å³/Da / Density % sol: 55.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 16% PEG 1000, 0.1 M sodium acetate pH 3.5, 0.2 M zinc acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 6, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 40695 / % possible obs: 97.4 % / Redundancy: 3 % / R_merge(I) obs: 0.084 / Net I/σ(I): 20.2
Reflection shell	Resolution: 2.5→2.54 Å

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5H5V

5h5v

Resolution: 2.5→30 Å / Cor.coef. F_o:F_c: 0.923 / Cor.coef. F_o:F_c free: 0.887 / Cross valid method: THROUGHOUT / ESU R: 0.499 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27847	2006	4.9 %	RANDOM
R_work	0.22897	-	-	-
obs	0.23144	38651	97.43 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 40.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7091	0	0	85	7176

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	7121
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	4381
X-RAY DIFFRACTION	r_angle_refined_deg	1.115	1.965	9697
X-RAY DIFFRACTION	r_angle_other_deg	4.557	3	10984
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.013	5	971
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.075	27.701	261
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.448	15	1256
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.639	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	1289
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	7946
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1126
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	0.204	1.5	4835
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	1987
X-RAY DIFFRACTION	r_mcangle_it	0.41	2	7836
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.879	3	2286
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.598	4.5	1861
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	386	medium positional	0.25	0.5
1	1	B	386	medium positional	0.23	0.5
1	1	C	386	medium positional	0.19	0.5
1	1	D	386	medium positional	0.2	0.5
1	1	E	386	medium positional	0.16	0.5
2	2	A	688	medium positional	0.18	0.5
2	2	B	688	medium positional	0.3	0.5
2	2	C	688	medium positional	0.21	0.5
2	2	D	688	medium positional	0.22	0.5
2	2	E	688	medium positional	0.25	0.5
1	1	A	333	loose positional	0.35	5
1	1	B	333	loose positional	0.36	5
1	1	C	333	loose positional	0.32	5
1	1	D	333	loose positional	0.29	5
1	1	E	333	loose positional	0.29	5
2	2	A	681	loose positional	0.29	5
2	2	B	681	loose positional	0.4	5
2	2	C	681	loose positional	0.34	5
2	2	D	681	loose positional	0.37	5
2	2	E	681	loose positional	0.36	5
1	1	A	386	medium thermal	0.23	2
1	1	B	386	medium thermal	0.16	2
1	1	C	386	medium thermal	0.08	2
1	1	D	386	medium thermal	0.12	2
1	1	E	386	medium thermal	0.15	2
2	2	A	688	medium thermal	0.19	2
2	2	B	688	medium thermal	0.19	2
2	2	C	688	medium thermal	0.18	2
2	2	D	688	medium thermal	0.15	2
2	2	E	688	medium thermal	0.15	2
1	1	A	333	loose thermal	0.35	10
1	1	B	333	loose thermal	0.25	10
1	1	C	333	loose thermal	0.19	10
1	1	D	333	loose thermal	0.2	10
1	1	E	333	loose thermal	0.23	10
2	2	A	681	loose thermal	0.37	10
2	2	B	681	loose thermal	0.29	10
2	2	C	681	loose thermal	0.26	10
2	2	D	681	loose thermal	0.26	10
2	2	E	681	loose thermal	0.27	10

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.389	158	-
R_work	0.317	2847	-
obs	-	-	99.21 %

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	7.4598	1.1373	-1.2901	4.0401	-0.4243	1.4653	-0.0633	-0.1381	0.1605	-0.0069	-0.0066	-0.2627	0.1204	0.0173	0.07	0.0586	0.0254	-0.0381	0.175	0.0022	0.3234	-40.305	48.06	7.001
2	18.7032	-2.463	0.5966	4.9035	0.6674	0.4519	0.4007	-0.4504	-1.5013	0.1973	0.0588	0.1079	0.3015	0.0233	-0.4595	0.283	-0.0136	-0.2298	0.4011	0.0694	0.9246	-11.963	55.596	7.847
3	3.5885	2.6816	-1.0398	9.1017	-2.0886	5.0523	-0.1814	0.1353	0.0871	-0.0396	0.2152	0.5936	0.1132	-0.1814	-0.0337	0.1033	-0.0333	0.0102	0.3989	0.0179	0.4231	-3.235	37.184	25.868
4	9.0724	5.3123	0.8908	7.2317	-1.2987	4.6981	-0.7581	1.5409	0.3229	-0.9071	1.0061	0.3712	-0.0543	-0.5186	-0.2481	0.2791	-0.0901	-0.0349	0.8098	0.2097	0.5089	-21.172	14.546	28.484
5	7.431	-0.8827	0.6749	3.9437	-1.9996	4.7821	0.2347	-0.1318	0.1806	0.1013	-0.1001	-0.7655	0.0026	0.1675	-0.1347	0.062	0.0224	-0.0554	0.3302	0.0542	0.6282	-44.819	22.578	15.445
6	3.817	2.477	0.4925	5.0074	1.038	1.2837	0.0202	-0.173	-0.0445	-0.0618	-0.0805	0.0925	0.0101	-0.0919	0.0603	0.0199	0.0015	-0.0024	0.2464	0.0237	0.2632	-65.109	24.566	7.921
7	5.665	-0.4989	-0.6472	3.3385	-1.6298	2.0089	0.1031	0.4773	0.63	-0.2055	-0.0136	-0.1387	-0.1604	-0.0797	-0.0894	0.092	0.0209	0.0641	0.2771	0.0675	0.4833	-42.046	67.834	-3.359
8	6.8807	-0.2019	0.464	4.2172	-1.0714	2.8787	0.2435	0.4491	0.5525	-0.1738	-0.1437	-0.1154	-0.0742	0.0771	-0.0999	0.0608	0.0573	0.0412	0.2953	0.0003	0.4542	7.484	64.482	8.559
9	5.4204	2.4501	-0.7876	3.5971	-0.748	2.2982	-0.1191	-0.3686	-0.5514	0.316	0.0635	-0.3083	-0.0218	0.4346	0.0556	0.2052	0.0085	0.0109	0.4726	-0.0256	0.4075	9.998	25.025	39.065
10	5.4588	-1.6932	1.7997	6.1048	-1.1175	2.3885	-0.3322	-0.6087	-0.5934	0.0332	0.4705	0.5299	0.0202	-0.1958	-0.1382	0.1358	0.0699	0.0036	0.6308	0.2347	0.5588	-32.46	-2.271	35.721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	72 - 103
2	X-RAY DIFFRACTION	1	A	226 - 267
3	X-RAY DIFFRACTION	2	B	72 - 103
4	X-RAY DIFFRACTION	2	B	226 - 266
5	X-RAY DIFFRACTION	3	C	72 - 103
6	X-RAY DIFFRACTION	3	C	226 - 267
7	X-RAY DIFFRACTION	4	D	74 - 103
8	X-RAY DIFFRACTION	4	D	226 - 266
9	X-RAY DIFFRACTION	5	E	72 - 103
10	X-RAY DIFFRACTION	5	E	226 - 267
11	X-RAY DIFFRACTION	6	A	104 - 225
12	X-RAY DIFFRACTION	7	B	104 - 225
13	X-RAY DIFFRACTION	8	C	104 - 225
14	X-RAY DIFFRACTION	9	D	104 - 225
15	X-RAY DIFFRACTION	10	E	104 - 225

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