PDB-6ch2: Crystal structure of the cytoplasmic domain of FlhA and FliT-FliD...

ID or keywords:

Entry

Database: PDB / ID: 6ch2

Title

Crystal structure of the cytoplasmic domain of FlhA and FliT-FliD complex

Components

Flagellar biosynthesis protein FlhA
Flagellar hook-associated protein 2,Flagellar protein FliT

Keywords

STRUCTURAL PROTEIN / flagellar

Function / homology

Function and homology information

negative regulation of bacterial-type flagellum assembly / bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum organization / bacterial-type flagellum assembly / protein secretion / bacterial-type flagellum-dependent cell motility / protein folding / cell adhesion / extracellular region ...
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Salmonella typhi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Xing, Q. / Shi, K. / Kalodimos, C.G.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM118047	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM073854	United States

Citation

Journal: Nat Commun / Year: 2018
Title: Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system.
Authors: Xing, Q. / Shi, K. / Portaliou, A. / Rossi, P. / Economou, A. / Kalodimos, C.G.

History

Deposition	Feb 21, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 16, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 4, 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	6ch2.cif.gz	568.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6ch2.ent.gz	474.5 KB	Display	PDB format
PDBx/mmJSON format	6ch2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ch2_validation.pdf.gz	491.9 KB	Display	wwPDB validaton report
Full document	6ch2_full_validation.pdf.gz	509.8 KB	Display
Data in XML	6ch2_validation.xml.gz	48.5 KB	Display
Data in CIF	6ch2_validation.cif.gz	65.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ch/6ch2 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6ch2	HTTPS FTP

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Related structure data

Related structure data	6ch1C 6ch3C 3a5iS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6osu-d 5jjw-d 2dxi-2 1n78-2 6j72-d 4jrl-1 5dhg-3 1n77-2 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

6ch1C

6ch3C

3a5iS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Flagellar biosynthesis protein FlhA

B: Flagellar biosynthesis protein FlhA

C: Flagellar biosynthesis protein FlhA

D: Flagellar hook-associated protein 2,Flagellar protein FliT

E: Flagellar hook-associated protein 2,Flagellar protein FliT

F: Flagellar hook-associated protein 2,Flagellar protein FliT

hetero molecules

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

1

A: Flagellar biosynthesis protein FlhA

D: Flagellar hook-associated protein 2,Flagellar protein FliT

hetero molecules

defined by author
Evidence: gel filtration, A and D B and E C and F
56.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Flagellar biosynthesis protein FlhA

E: Flagellar hook-associated protein 2,Flagellar protein FliT

hetero molecules

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

3

C: Flagellar biosynthesis protein FlhA

F: Flagellar hook-associated protein 2,Flagellar protein FliT

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

Unit cell

Length a, b, c (Å)	49.110, 77.590, 119.270
Angle α, β, γ (deg.)	86.88, 89.00, 84.27
Int Tables number	1
Space group name H-M	P1

#1: Protein	Flagellar biosynthesis protein FlhA Mass: 36740.309 Da / Num. of mol.: 3 / Fragment: unp residues 360-692 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: flhA, STM1913 / Production host: Escherichia coli (E. coli) / References: UniProt: P40729
#2: Protein	Flagellar hook-associated protein 2,Flagellar protein FliT / HAP2 / Filament cap protein / Flagellar cap protein Mass: 19555.023 Da / Num. of mol.: 3 / Fragment: unp residues 1-122; 428-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Salmonella typhi (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliD, flaV, flbC, STM1960, fliT, STY2170, t0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P16328, UniProt: P0A1N3
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.68 Å³/Da / Density % sol: 54.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: CaCl2, PEG8000, Sodium cacodylate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jul 10, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.7→39.695 Å / Num. obs: 44673 / % possible obs: 92.98 % / Redundancy: 2.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / R_sym value: 0.054 / Net I/σ(I): 9.16
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.1 / CC_1/2: 0.62 / R_sym value: 0.74 / % possible all: 93.68

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2747: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3A5I

3a5i

Resolution: 2.7→39.695 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2662	1990	4.46 %
R_work	0.2334	-	-
obs	0.2348	44667	93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.7→39.695 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11161	0	12	41	11214

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11337
X-RAY DIFFRACTION	f_angle_d	0.547	15354
X-RAY DIFFRACTION	f_dihedral_angle_d	16.161	4307
X-RAY DIFFRACTION	f_chiral_restr	0.057	1801
X-RAY DIFFRACTION	f_plane_restr	0.003	1996

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 (%)
2.7-2.7675	0.4203	147	0.4422	3080	X-RAY DIFFRACTION	94
2.7675-2.8423	0.4174	144	0.3883	3074	X-RAY DIFFRACTION	93
2.8423-2.9259	0.4034	140	0.3626	3048	X-RAY DIFFRACTION	93
2.9259-3.0203	0.3695	138	0.3493	3031	X-RAY DIFFRACTION	93
3.0203-3.1282	0.375	135	0.3411	2966	X-RAY DIFFRACTION	90
3.1282-3.2534	0.3795	142	0.3135	3059	X-RAY DIFFRACTION	93
3.2534-3.4014	0.3217	148	0.2952	3097	X-RAY DIFFRACTION	95
3.4014-3.5807	0.3106	142	0.261	3052	X-RAY DIFFRACTION	94
3.5807-3.8048	0.2781	145	0.2422	3093	X-RAY DIFFRACTION	93
3.8048-4.0983	0.2527	139	0.2198	2991	X-RAY DIFFRACTION	91
4.0983-4.5102	0.2482	144	0.1905	3028	X-RAY DIFFRACTION	92
4.5102-5.1617	0.1911	142	0.1836	3059	X-RAY DIFFRACTION	93
5.1617-6.4985	0.2598	138	0.2149	2997	X-RAY DIFFRACTION	92
6.4985-39.6991	0.1846	146	0.1601	3102	X-RAY DIFFRACTION	94

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	0.1323	-0.0677	0.0893	0.1258	0.0289	0.2819	-0.0382	0.0204	-0.467	0.1866	-0.0829	0.2453	0.2748	-0.0092	-0.0115	0.5694	0.058	-0.1001	0.4023	0.134	0.4891	-3.9704	-43.929	-9.7376
2	0.3928	-0.0422	0.3305	0.1513	-0.1196	0.4173	-0.0658	0.0823	-0.1279	0.0588	0.1747	-0.0298	-0.1117	0.133	-0	0.3996	-0.0449	0.0032	0.5817	-0.0794	0.3896	20.8008	-25.6326	-13.2602
3	-0.0107	0.0745	0.0362	0.0952	0.0265	0.0278	0.1162	-0.061	0.3593	-0.0648	0.118	-0.185	-0.0865	0.3101	0	0.6423	-0.1041	0.0643	0.5765	0.0061	0.5467	5.0811	-30.6504	-51.0602
4	0.0452	0.0283	-0.0292	0.0306	-0.003	0.045	-0.0363	-0.233	0.3308	-0.0523	0.2371	0.2359	0.0283	-0.1428	0.0001	0.586	-0.0016	-0.0459	0.4681	0.0957	0.3801	-1.3589	-35.8891	-46.3061
5	0.0355	0.0048	-0.0048	0.0693	-0.0352	0.0125	0.1414	0.0537	0.0378	0.1458	-0.0938	-0.0074	-0.1477	0.4271	0	0.462	-0.0492	0.0508	0.5333	0.0009	0.4602	13.2117	-50.615	-57.358
6	0.2152	0.027	-0.1464	-0.0036	0.0519	0.1939	-0.0749	-0.5319	0.2356	-0.0717	-0.0131	0.4119	-0.5498	0.3167	0.008	0.8021	0.0951	-0.1095	0.2809	-0.093	0.7566	-11.5962	-26.6706	-59.7483
7	0.0205	-0.0129	0.0091	0.0366	0.0444	0.0395	-0.338	-0.1591	0.024	0.0112	-0.0895	0.2665	-0.3172	-0.0671	0	0.6707	0.0962	-0.2193	0.5019	0.0883	0.7818	-22.3812	-28.2835	-67.9661
8	0.026	-0.0605	0.0263	0.0663	-0.0287	-0.007	-0.0138	0.3467	0.1307	-0.0404	-0.0884	-0.0871	0.1676	-0.0733	0	0.5026	0.0433	0.1015	0.6873	0.0077	0.6986	-19.6637	-45.8792	-77.8712
9	0.0857	0.0066	0.0301	0.1057	0.0233	0.0723	0.0049	0.5372	-0.433	-0.0201	-0.1154	-0.1287	0.1034	-0.0196	0	0.4552	0.1225	-0.045	0.6516	0.0931	0.4837	-16.0681	-48.5824	-74.245
10	0.0555	0.0563	0.0138	0.0451	0.0377	0.0359	-0.2568	0.1473	-0.0909	0.0425	0.1599	0.2994	0.0574	0.0888	0	0.7393	-0.0265	-0.0425	0.6313	-0.0615	0.7796	-1.7534	19.0011	-29.3033
11	0.3219	0.2036	0.0384	0.0705	-0.0324	0.1918	-0.1079	0.1638	-0.0519	0.1305	-0.1748	0.1633	0.0521	-0.2815	-0.1096	0.5706	-0.0648	0.1393	0.3629	0.0202	0.4938	-6.6916	6.7933	-32.8541
12	0.1557	-0.1884	0.0134	0.1652	0.13	0.0996	0.136	0.1109	-0.1696	-0.0513	-0.3274	0.7051	-0.1078	0.0802	-0.0003	0.8421	-0.0859	0.0711	0.4576	-0.0815	0.7325	-1.8478	-13.6093	-38.9147
13	0.0542	-0.0874	0.0904	0.5877	-0.4824	0.4056	-0.0564	-0.2927	0.4883	-0.3308	0.0942	-0.1257	0.1988	-0.0475	0.04	0.4591	-0.0155	0.1048	0.8324	-0.3504	0.9619	-2.2452	-0.2001	8.9035
14	0.1417	-0.1203	0.0466	0.1497	-0.1878	0.6429	0.1813	-0.7643	0.5501	-0.0034	0.0816	0.0289	0.308	-0.1712	0.6017	0.0705	0.0526	0.2779	0.6428	-0.5407	0.8627	-9.0961	3.0044	13.5991
15	0.2675	0.2308	0.0006	0.442	-0.4462	0.8268	-0.121	1.0946	-0.6884	0.0538	0.018	0.1014	-0.4001	-0.195	0.0971	0.0659	-0.0418	0.0689	1.2812	-0.6837	0.9576	8.7793	-68.0679	-97.9383
16	0.1161	-0.0194	-0.1499	0.5617	0.1034	0.4278	0.1743	0.4209	-0.3764	0.1667	0.0136	-0.1043	-0.0791	-0.069	0.0829	0.3588	0.0143	-0.0362	0.958	-0.4677	0.9339	8.7149	-67.0569	-92.9665
17	-0.0011	0.0087	-0.0107	0.0072	-0.0047	0.0108	0.0761	0.0625	0.1493	-0.1727	0.0082	0.0576	0.1932	0.0592	0.0002	1.894	0.0678	0.2866	1.0125	-0.1301	1.2157	-8.2295	-9.8536	-69.2267
18	-0.0016	-0.0104	0.0149	0.0097	-0.0125	0.014	-0.0652	0.0263	-0.1168	0.0651	-0.2451	-0.05	-0.0029	0.106	0	1.9596	-0.0403	-0.0605	1.3565	-0.1499	1.4437	-7.2805	-12.5061	-89.2709
19	0.0066	-0.005	0.0213	-0.0038	0.0072	0.0124	-0.1194	0.0104	-0.2711	0.066	-0.0621	-0.0648	0.1093	0.0317	-0	1.6444	-0.1586	-0.0848	1.1081	-0.0335	1.3497	-9.7769	-18.9046	-87.2826
20	-0.0325	-0.0247	0.0577	0.1014	-0.1084	0.0791	0.3083	0.6279	0.1145	-0.061	-0.3312	0.0969	0.07	0.4155	0	1.0839	0.2059	-0.1361	1.1642	-0.1416	0.6922	-2.647	-3.4763	-69.0449

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 360 through 498 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 499 through 690 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 359 through 397 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 398 through 431 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 432 through 479 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 480 through 533 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 534 through 581 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 582 through 621 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 622 through 690 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 360 through 431 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 432 through 564 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 565 through 690 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 5 through 41 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 42 through 164 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 4 through 83 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 84 through 165 )
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 4 through 35 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 36 through 86 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 87 through 117 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 118 through 173 )

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