PDB-7eha: Crystal structure of the flagellar hook cap from Salmonella enter...

ID or keywords:

Entry

Database: PDB / ID: 7eha

Title

Crystal structure of the flagellar hook cap from Salmonella enterica serovar Typhimurium

Components

Basal-body rod modification protein FlgD

Keywords

MOTOR PROTEIN / Bacterial flagellum / Hook / Hook cap / Salmonella enterica serovar Typhimurium

Function / homology

FlgD Tudor-like domain / FlgD Tudor-like domain / Flagellar hook capping protein / Flagellar hook capping protein - N-terminal region / FlgD Ig-like domain / FlgD Ig-like domain / bacterial-type flagellum organization / Basal-body rod modification protein FlgD

Function and homology information

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.3 Å

Authors

Matsunami, H. / Yoon, Y.-H. / Imada, K. / Namba, K. / Samatey, F.A.

Funding support

Japan, 1items

Citation

Journal: Commun Biol / Year: 2021
Title: Structure of the bacterial flagellar hook cap provides insights into a hook assembly mechanism
Authors: Matsunami, H. / Yoon, Y.H. / Imada, K. / Namba, K. / Samatey, F.A.

History

Deposition	Mar 29, 2021	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Nov 24, 2021	ID: 6IEE
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 / _struct_ncs_dom_lim.selection_details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7eha.cif.gz	380.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7eha.ent.gz	267.2 KB	Display	PDB format
PDBx/mmJSON format	7eha.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/eh/7eha ftp://data.pdbj.org/pub/pdb/validation_reports/eh/7eha	HTTPS FTP

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Related structure data

Related structure data	7eh9C C: citing same article (ref.)
Similar structure data	4kqe-1 6qib-d 6i8a-1 4m8o-d 6h1v-d 6fwk-1 4ptf-d 4ghk-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: Basal-body rod modification protein FlgD

B: Basal-body rod modification protein FlgD

C: Basal-body rod modification protein FlgD

D: Basal-body rod modification protein FlgD

E: Basal-body rod modification protein FlgD

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

1

Idetical with deposited unit
defined by author&software
Evidence: cross-linking

Unit cell

Length a, b, c (Å)	141.283, 141.283, 153.487
Angle α, β, γ (deg.)	90.0, 90.0, 120.0
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	LYS	LYS	chain 'B' and segid 'B '	B	B	68 - 112	68 - 112
1	2	VAL	VAL	GLN	GLN	chain 'B' and segid 'B '	B	B	119 - 130	119 - 130
1	3	ALA	ALA	THR	THR	chain 'B' and segid 'B '	B	B	133 - 164	133 - 164
1	4	LYS	LYS	VAL	VAL	chain 'B' and segid 'B '	B	B	168 - 206	168 - 206
1	5	LEU	LEU	ILE	ILE	chain 'B' and segid 'B '	B	B	215 - 232	215 - 232
2	6	VAL	VAL	LYS	LYS	chain 'C' and segid 'C '	C	C	68 - 112	68 - 112
2	7	VAL	VAL	GLN	GLN	chain 'C' and segid 'C '	C	C	119 - 130	119 - 130
2	8	ALA	ALA	THR	THR	chain 'C' and segid 'C '	C	C	133 - 164	133 - 164
2	9	LYS	LYS	VAL	VAL	chain 'C' and segid 'C '	C	C	168 - 206	168 - 206
2	10	LEU	LEU	ILE	ILE	chain 'C' and segid 'C '	C	C	215 - 232	215 - 232
3	11	VAL	VAL	LYS	LYS	chain 'D' and segid 'D '	D	D	68 - 112	68 - 112
3	12	VAL	VAL	GLN	GLN	chain 'D' and segid 'D '	D	D	119 - 130	119 - 130
3	13	ALA	ALA	THR	THR	chain 'D' and segid 'D '	D	D	133 - 164	133 - 164
3	14	LYS	LYS	VAL	VAL	chain 'D' and segid 'D '	D	D	168 - 206	168 - 206
3	15	LEU	LEU	ILE	ILE	chain 'D' and segid 'D '	D	D	215 - 232	215 - 232
4	16	VAL	VAL	LYS	LYS	chain 'E' and segid 'E '	E	E	68 - 112	68 - 112
4	17	VAL	VAL	GLN	GLN	chain 'E' and segid 'E '	E	E	119 - 130	119 - 130
4	18	ALA	ALA	THR	THR	chain 'E' and segid 'E '	E	E	133 - 164	133 - 164
4	19	LYS	LYS	VAL	VAL	chain 'E' and segid 'E '	E	E	168 - 206	168 - 206
4	20	LEU	LEU	ILE	ILE	chain 'E' and segid 'E '	E	E	215 - 232	215 - 232

#1: Protein	Basal-body rod modification protein FlgD / Flagellar hook cap Mass: 24001.637 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Gene: flgD, fla FIV, flaV, STM1176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1I9

#1: Protein

Basal-body rod modification protein FlgD / Flagellar hook cap

Mass: 24001.637 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: flgD, fla FIV, flaV, STM1176 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1I9

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.68 Å³/Da / Density % sol: 66.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 5.6 / Details: PEG 2000, sodium citrate, 2,3-butanediol, glycerol

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Data collection

Diffraction	Mean temperature: 40 K / Ambient temp details: Helium gas flow / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.3→47.8 Å / Num. obs: 27142 / % possible obs: 100 % / Redundancy: 14.3 % / R_merge(I) obs: 0.109 / Net I/σ(I): 19
Reflection shell	Resolution: 3.3→3.48 Å / R_merge(I) obs: 0.401 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3930

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Processing

Software

Name	Version	Classification
BSS		data collection
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing
PHENIX	1.9_1692	refinement

Refinement

Method to determine structure:

MAD / Resolution: 3.3→47.2 Å / SU ML: 0.392618180736 / Cross valid method: FREE R-VALUE / σ(F): 1.37992078097 / Phase error: 27.8411812832

	R_factor	Num. reflection	% reflection
R_free	0.284	2589	5.02162654926 %
R_work	0.244	48968	-
obs	0.246	27142	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 137.22 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→47.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5988	0	0	0	5988

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00349837902806	6045
X-RAY DIFFRACTION	f_angle_d	0.779841890521	8236
X-RAY DIFFRACTION	f_chiral_restr	0.0296680664753	1051
X-RAY DIFFRACTION	f_plane_restr	0.00314458021529	1065
X-RAY DIFFRACTION	f_dihedral_angle_d	12.0916738323	2138

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 (%)
3.3-3.3635	0.299723526193	147	0.274471417298	2776	X-RAY DIFFRACTION	100
3.3635-3.4322	0.310192277136	132	0.263797111833	2700	X-RAY DIFFRACTION	100
3.4322-3.5068	0.320713536296	186	0.261002845724	2669	X-RAY DIFFRACTION	100
3.5068-3.5883	0.287658197005	102	0.275771708341	2748	X-RAY DIFFRACTION	100
3.5883-3.678	0.337272506985	167	0.28193140797	2689	X-RAY DIFFRACTION	100
3.678-3.7774	0.338087494073	158	0.286642729296	2751	X-RAY DIFFRACTION	100
3.7774-3.8885	0.311156965301	174	0.276538974346	2671	X-RAY DIFFRACTION	100
3.8885-4.014	0.279910981253	154	0.273121586276	2754	X-RAY DIFFRACTION	100
4.014-4.1574	0.330696474202	156	0.25015519538	2691	X-RAY DIFFRACTION	100
4.1574-4.3237	0.267315746346	110	0.236924445395	2702	X-RAY DIFFRACTION	100
4.3237-4.5203	0.227027307122	152	0.22517899329	2745	X-RAY DIFFRACTION	100
4.5203-4.7584	0.202952269782	128	0.201295669348	2731	X-RAY DIFFRACTION	100
4.7584-5.0563	0.23388837818	124	0.202274062063	2743	X-RAY DIFFRACTION	100
5.0563-5.4461	0.251585792009	164	0.220392399166	2711	X-RAY DIFFRACTION	100
5.4461-5.9932	0.25266526196	114	0.238610285882	2715	X-RAY DIFFRACTION	100
5.9932-6.8582	0.320334192741	134	0.276869944114	2734	X-RAY DIFFRACTION	100
6.8582-8.632	0.273301824469	124	0.247877538086	2731	X-RAY DIFFRACTION	99.6509598604
8.632-47.2	0.313124351727	163	0.241537316369	2707	X-RAY DIFFRACTION	99.7220291869

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	0.0530110354193	-0.124440189208	-0.0668284025128	0.0678008869117	0.0359015992271	0.0600295151099	0.259897140884	0.504927617566	-1.76186773533	-0.257942270487	0.740990311948	-1.03530600861	0.307050069705	0.731216813855	0.0377777128122	1.76156023501	0.285785040469	-0.667725952511	1.12165079981	-0.259165870505	3.42171538665	-16.7971934396	24.1509558385	-4.190714562
2	2.58854719309	1.06210258846	1.57051542282	3.45968708737	-1.13873914503	5.90530766339	-0.386122807289	-0.288018717466	0.197552310695	-0.036037753197	-0.226354833994	-0.215885635177	-0.455687237171	-0.485047273867	-0.00194940972072	0.496025006807	-0.0997115922027	-0.17782727112	0.660806895534	0.0444978993992	0.554230713886	-39.547259136	63.3102329877	-12.7038074973
3	5.64679229606	-3.09260878032	-1.48236454001	1.80666315716	0.778971066456	0.337829700725	-0.635164714615	-1.04537016191	0.737326267514	-0.59223908285	0.874305479139	-1.2650905905	1.65524453983	0.787134863655	0.257688880864	1.82587597222	0.12625789352	0.113192509138	1.25439362631	0.220370696091	1.67375672518	-22.2578839159	28.6983752196	3.91721841574
4	1.12740270213	-0.249261372436	0.684165398646	0.925834577387	-0.368541189697	0.817287671515	0.0593947939753	0.563979592735	0.685448019636	-0.990383575888	-0.348066293865	0.166847809885	-0.722851102684	0.222943419172	-0.0614544763269	1.56247185724	-0.511121196692	-0.327265226166	0.781600722348	0.385079368565	1.15931455091	-58.4604579232	37.3012191736	-9.17744719769
5	0.88904689869	-0.00508427171941	0.382091668774	0.957362929596	-0.72907559111	0.731390376856	0.595036358911	-0.0635890778643	-0.350867657207	-0.0326732696445	-0.404049135358	-0.521021923364	0.578840071703	0.256999682271	0.173571603713	1.37561933669	-0.720962065903	-0.213845853288	1.21651906401	0.636778308153	1.22896932026	-43.4951109721	30.6157316122	-2.492391834
6	0.0157373760429	-0.133056711416	0.0156166511043	0.50614286607	-0.205028266862	0.0477956565383	0.520880087378	-0.0557347751514	-0.171897371335	-0.733346912906	-0.152035915972	-1.82917790009	1.01423175684	0.995351894548	0.0947499391185	1.27253501748	0.0481944816537	0.158394443717	1.91003406444	0.365666486967	2.31137312503	-9.36294205274	37.5535746046	5.39713227272
7	0.104296977351	-0.243645642949	0.330364213454	0.431308599284	-0.601407689193	0.859144921384	-0.187554399096	0.27408676879	0.114815034028	0.455755107111	-0.571867884027	-0.503848894057	-0.511909113249	0.893492454647	-0.877930610779	1.21706216158	-1.27181071606	-0.0960404917475	1.36464112899	1.3071579623	0.920936616767	-44.0193356349	22.5073600753	24.1906306943
8	0.595673173052	-0.828034593565	-0.468424419717	1.57099726647	0.187849919756	2.01851508938	-0.403975010596	-0.09512746385	-0.0311005934196	0.625555989821	-0.537247872866	-0.133794379984	-0.634467912423	1.36365849107	-1.67112573854	1.10784757155	-0.803966827008	-0.221637636339	1.47906389433	0.961467984526	1.07249496345	-42.7194525521	21.8479457832	26.4088193336
9	-0.000672436909137	0.00368610645736	0.00497713453048	0.00187730202951	-0.0023655296714	0.0354845775133	-0.032481640822	0.140710812752	0.0673151540484	0.0876716332267	-0.0255609504967	-0.131715392707	0.0183016302177	0.0119228681244	-0.438748953966	1.4633342474	-1.17731479512	-0.605424681233	2.32339523333	1.47000088765	1.93974737698	-29.9656368117	30.8974856906	20.5446855283
10	0.4542582082	-0.68700823233	0.198120192452	1.01869498748	-0.347318597277	0.311821230636	0.973523346614	0.967919276049	-0.554437657702	-1.10376870271	0.403466437363	-1.13457891317	1.35873171297	1.44684585254	0.393034750796	0.92694002367	0.0404153413083	0.0477928927248	2.17882972512	0.0593661911129	1.67641549091	-10.8415227884	44.7449574846	0.0480082224592
11	0.0565551776879	0.0184134149667	-0.0729834310463	0.325815979522	-0.010969503843	0.26213672071	-0.686024676994	-0.224265408791	-0.361644904935	1.01022691842	0.571537398333	-0.37622294811	0.861658288448	-0.403423916187	-0.0263882176456	1.84802873415	-0.278636930474	-0.550781045349	1.8216806598	0.313585195208	1.02570619169	-17.5153082288	44.6974852281	32.4975076136
12	0.0222652029833	0.0303016605159	-0.0271218803905	0.0300473118449	-0.0317936536689	0.0287943003382	0.120086670112	-0.179874952844	0.59450585728	0.0261069515795	0.262883496033	-0.649768779723	-0.109224331945	0.0130030458847	-4.26913279129E-5	2.34507337258	-0.592155503742	-0.0507486343411	2.20824698959	0.157641383491	1.1936724682	-13.5442473956	50.765189671	45.6213662627
13	1.17562229734	0.835002991032	0.538965975878	0.600214300075	0.386301407581	0.249109455467	0.0819612295003	-0.0154446650564	-0.614832905867	0.143434759684	0.119312687628	-0.356201415622	0.386879888415	0.157926243705	-0.220263302087	2.50517741536	-0.345437787142	-0.529545397096	1.70683576941	0.528399656074	1.11286941223	-16.7327298055	33.5089930791	33.49299485
14	0.177975318007	-0.0295840620922	0.152452228103	0.0248693538529	-0.0335366493131	0.112881371118	-0.292060240509	-1.52206488492	-0.359663593795	0.815517436515	0.281515370456	-0.876700778364	1.14968621275	0.815403273081	0.00212034884277	1.64660397672	-0.0285477564739	-0.536376408826	1.89407789852	0.556267768196	1.84937615943	-14.0977844634	43.5491918898	40.7271953206
15	0.0579685084475	0.107274312363	-0.0248157142685	0.849019774041	1.0216857426	1.91115146565	-0.107592141882	-0.610324011342	-0.299301733263	0.595629031178	-0.339160224854	-1.1264744487	0.373657187742	1.99551225338	0.783619806285	1.1724751621	-0.333980412024	-0.623892128653	1.36682867536	0.720181943259	1.36722712142	-15.4152240249	50.6777206501	19.4595836526
16	0.0371320311581	-0.0514559811533	0.0391378889114	0.140140113524	-0.100272898829	0.0637256773827	0.500831229231	1.25918604184	-0.230081047329	-0.955677242918	-0.571190235966	-0.928252128851	1.32953307823	2.13205763479	0.00769765927855	1.60067349257	0.696997691417	-0.0441129858628	2.07483006129	-0.0165654510686	1.47636100467	-14.8109729691	41.4672005501	-7.8885284049
17	2.35110477354	0.666865629446	-0.623365981359	3.8667366822	2.27151371993	1.78722888679	-0.375590641307	0.00215970922086	0.624994862724	-0.130320109401	-0.610497528885	0.989557374479	-0.611594779461	-0.446768839346	-0.306159701729	0.571204976288	-0.308104451509	-0.380490083751	0.714462355193	0.189046322089	0.95022901668	-24.6332897424	67.8643167797	8.36360042231
18	2.59807136152	0.0247695081562	-0.47316889016	0.0102068881233	-0.222573165099	4.52584891236	-0.114471641459	-0.300597315175	0.107641290967	0.344882411724	-0.124252459157	0.993069973188	-0.600536781299	-2.00846767015	-0.27966919593	1.13147532862	-0.461050857793	0.032410830052	1.22023719381	0.0919244963164	1.48064257316	-36.9723850804	73.7040450622	18.6661477181
19	2.47363431835	1.07559723387	0.23127923783	2.28573604089	-0.779752154971	1.24057295521	0.0315600043112	-0.439805416475	0.269936787924	1.17359391853	-0.424531505666	-0.29403802083	-0.508540577357	0.454485076697	-0.0297442880638	0.936851121326	-0.287761996889	-0.369146406703	0.972664739525	0.297077782805	0.828992744471	-18.412256262	71.8083711631	11.9036359865

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 56 through 96 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 97 through 232 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 62 through 104 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 105 through 187 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 188 through 232 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 63 through 98 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 99 through 163 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 164 through 206 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 215 through 232 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 68 through 96 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 97 through 141 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 142 through 150 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 151 through 163 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 164 through 195 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 196 through 232 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 67 through 96 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 97 through 110 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 111 through 124 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 125 through 232 )

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