PDB-7eh9: Crystal structure of the flagellar hook cap fragment from Salmone...

ID or keywords:

Entry

Database: PDB / ID: 7eh9

Title

Crystal structure of the flagellar hook cap fragment 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 /

SAD / Resolution: 2.2 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: 6IEF
Revision 1.0	Nov 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7eh9.cif.gz	141.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7eh9.ent.gz	92 KB	Display	PDB format
PDBx/mmJSON format	7eh9.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/7eh9 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/7eh9	HTTPS FTP

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Related structure data

Related structure data	7ehaC C: citing same article (ref.)
Similar structure data	2lpe-d 4ety-2 4esk-4 6he6-2 2h41-d 2h41-1 6hfx-2 6mk7-d 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

Deposited unit

A: Basal-body rod modification protein FlgD

B: Basal-body rod modification protein FlgD

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

1

A: Basal-body rod modification protein FlgD

defined by author
Evidence: gel filtration
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Basal-body rod modification protein FlgD

defined by author
18.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	75.9852, 104.323, 43.867
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Basal-body rod modification protein FlgD / Flagellar hook-capping protein Mass: 18708.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: flgD, fla FIV, flaV, STM1176 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A1I9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.32 Å³/Da / Density % sol: 47.06 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: PEG 3350, ammonium citrate dibasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 16, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→35.7 Å / Num. obs: 18336 / % possible obs: 99.8 % / Redundancy: 7.1 % / R_merge(I) obs: 0.081 / Net I/σ(I): 14.6
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.272 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2615 / % possible all: 99.6

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.2→33.57 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.57

	R_factor	Num. reflection	% reflection
R_free	0.248	1756	5.23 %
R_work	0.199	31792	-
obs	0.202	18336	98.2 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→33.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1967	0	0	117	2084

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00705136993241	1989
X-RAY DIFFRACTION	f_angle_d	1.0283504304	2711
X-RAY DIFFRACTION	f_chiral_restr	0.0349870773635	345
X-RAY DIFFRACTION	f_plane_restr	0.00413516851453	347
X-RAY DIFFRACTION	f_dihedral_angle_d	13.779814799	699

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 (%)
2.2-2.2595	0.394879472432	110	0.243646635532	2615	X-RAY DIFFRACTION	94.7122861586
2.2595-2.3259	0.312878192417	133	0.243660417478	2366	X-RAY DIFFRACTION	95.1637471439
2.3259-2.401	0.289625089099	168	0.226238670964	2403	X-RAY DIFFRACTION	96.509009009
2.401-2.4868	0.274059894525	146	0.22458920345	2382	X-RAY DIFFRACTION	96.7840735069
2.4868-2.5863	0.299163825273	115	0.226400884768	2466	X-RAY DIFFRACTION	97.2860912175
2.5863-2.704	0.320685835109	121	0.222790338861	2445	X-RAY DIFFRACTION	98.7302808773
2.704-2.8465	0.286366204232	107	0.213869622335	2506	X-RAY DIFFRACTION	98.6782477341
2.8465-3.0247	0.275705244124	145	0.211703356133	2461	X-RAY DIFFRACTION	99.3140243902
3.0247-3.2581	0.323697859852	147	0.207061576089	2474	X-RAY DIFFRACTION	99.6199163816
3.2581-3.5856	0.231024937208	137	0.193365480949	2510	X-RAY DIFFRACTION	99.9244998112
3.5856-4.1037	0.248835569168	154	0.184787392966	2472	X-RAY DIFFRACTION	100
4.1037-5.1671	0.185631195872	140	0.162843641757	2475	X-RAY DIFFRACTION	100
5.1671-33.57	0.223710785797	133	0.207032711505	2506	X-RAY DIFFRACTION	99.9621212121

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	1.84413783777	-1.4755808316	-0.211678368151	2.28665203587	-1.39075322833	2.1765071249	0.759190616761	0.7082313379	1.09791318135	-0.320198412304	-0.404309716572	-0.786055344837	-0.682497350316	0.0983506077765	0.142864699251	0.476475382047	0.0448236911325	0.0522527718711	0.541458982215	0.147346355104	1.11192719509	-24.7153678395	47.4172989486	-4.73649156946
2	1.97509182167	-0.379360658121	0.657046089894	3.66019540118	-0.764404514009	1.42151473323	-0.0843083668362	0.0777474306503	0.775065262856	0.105411440632	-0.468929408558	-1.55333257065	0.139784178257	0.23808758374	0.290678139015	0.352932813116	0.0856774946894	-0.0443527069691	0.360005950933	-0.0869564629325	0.457228493406	-25.2709262389	30.906192929	-0.547111871368
3	-0.00582436968274	-0.211717930132	-0.130531303144	0.731787756445	0.5589552682	0.434624917314	-0.344515685288	-0.664798474091	0.0914635600922	1.41103625855	0.235936413634	0.707277890374	-1.63043787196	-0.272182117246	0.645644480746	1.06269223132	0.184681756595	-0.0126098344849	0.729394564285	-0.110294523148	0.312774621645	-26.2813355361	25.6477584427	15.4689799167
4	2.84487774601	0.532617036026	0.597795923457	0.202362417778	0.418674902956	1.85833758683	0.686219055165	0.228172309768	-0.344704551687	-1.02328387203	0.051076639992	1.65410237296	0.475513578815	-0.292683398982	-0.500012927569	0.563012898148	0.0605423067428	-0.379562770061	0.52442524369	0.0781135534693	0.711647862436	-36.6026313939	20.9668301921	-7.70140321444
5	9.17466865819	-0.0590902228006	0.357610542869	6.17107272096	-0.107332318232	5.82365334573	0.662567193642	0.208816759008	-0.37558907518	0.088193349415	0.0251176465386	1.02472099021	0.779918267152	-0.455833018082	-0.332429893678	0.478132041403	-0.0156742816563	-0.051903403334	0.395336064571	0.0514376679878	0.58099876778	-27.1755213375	12.1963124334	1.9291461899
6	3.31554903043	-0.926456847506	-0.242812431859	3.53793506762	-1.53441101282	3.40282794731	0.071958744808	-0.783439924857	-0.626569726863	0.231225009437	0.76919627662	1.40777460135	0.16193897794	-1.2157449385	-0.688432980318	0.397300197191	0.0146661420894	-0.0808032358611	0.5733277972	0.119892233321	0.623110521201	-34.4385276289	20.1328758574	3.24396898366
7	3.07752023512	-2.18640885217	-0.861606273432	4.32680616873	-1.13995546127	2.19286583105	0.534198993677	0.276726511392	0.401114070884	-0.940134772173	-0.219708236213	0.149208261372	0.380561681102	-0.0361220913877	-0.0849055875173	0.476560307514	0.120637907201	-0.181712306319	0.352086210491	0.00097647296687	0.393817064132	-28.3134488611	23.0118389323	-4.29831693884
8	0.591082711061	1.98900624841	-0.825849843354	8.06445642938	-0.52808441982	4.19627587188	0.679198168868	0.341955380741	-0.747359003633	0.0667032492905	-0.323969976282	-0.996037414024	-0.33393126269	0.711797457669	-0.430485765424	0.405511672387	0.0815125218861	0.0648117417827	0.587348744906	-0.0314955906845	1.42625852671	-17.6767293197	37.924671438	-4.30366050401
9	4.33367446934	-0.373889054076	2.50837184616	3.5657838747	1.68677844913	2.72521902853	0.394974798495	0.397413309294	0.891816353616	-0.538060783576	-0.0806023907342	-0.844294122031	-0.0881609904199	0.840743765875	-0.210041126016	0.558024424058	0.0885306357179	0.0942395049697	0.400052563006	0.0172035255698	0.485837740395	-27.0506033932	36.5370393477	-7.61199798394
10	3.39287534007	-0.159895234659	-0.81871178221	2.37410212966	1.43035386629	1.0461393639	-0.176450976324	-0.320986607763	-0.0848329979314	0.127862935784	0.238426742061	0.00497924564332	-0.0763467580181	-0.0492761047312	-0.0744753391543	0.252827022006	0.0477301729297	-0.00194542751363	0.279776960628	0.0166127190966	0.197893265749	-3.50818410825	6.16535743092	-2.64575605185
11	5.11246262822	-1.08802626278	-4.43243989226	0.382275973996	1.10691401151	4.0315294297	0.313237880527	0.882942183157	0.691717525561	-0.342690219097	-0.16636559315	-0.158888202122	-0.907931104466	1.00653304496	-0.413923290028	0.652512997924	0.048261952133	-0.0793376534783	0.808040781224	0.0358338761397	0.390189389514	-10.4140612428	14.0746170716	-22.1836568672
12	3.83009838972	3.3273008206	-1.45045794921	3.87528043494	-0.998279341068	0.72871910498	0.500621448045	-0.666367383154	-0.77073798129	-0.669927357009	0.597443530988	2.40161885873	0.795059353823	-1.14821949825	0.444279546293	0.152261280387	0.109181908576	-0.31590625454	0.556866708602	0.380656866959	1.47355145941	-22.6655045713	-1.99973040839	-4.27641691788
13	3.38775174	0.330838574488	0.37157385549	4.9346603269	-1.12017365549	6.00886432433	0.658083747147	-0.885383261841	-1.52654687791	-0.196082397765	0.14525029498	1.40788118793	-0.383277820753	-1.05156214966	-0.293237321345	0.455872299364	0.181929730589	-0.336779779341	0.553987137176	0.285476935716	0.935840132914	-26.102498901	12.317599241	-13.1048207524
14	1.62595326174	-2.03669115868	1.16359969408	2.79571511408	-1.87554465558	3.2718070539	0.507170441068	0.366023024383	-1.07885462097	-0.717142045288	0.246947258968	1.52610524436	0.256842303948	-0.543563195523	-0.450923065954	0.59048420394	0.0516796107958	-0.243411500071	0.442464444356	0.0124980579663	0.685079630481	-21.1843907264	7.52864907124	-14.5581321044
15	9.13727678613	1.79592096482	0.505368300392	4.68143785611	0.016967221608	4.20944330939	0.602501462851	-0.647429915569	0.386659113807	0.37250826992	-0.107300016602	0.26359383827	-0.511197111392	-0.219157840473	-0.407293295136	0.316098141199	0.0127189893982	0.0326975430316	0.247016168915	0.0209543138608	0.321589588739	-6.96547757847	9.68890344682	0.850784849978
16	4.86206821626	0.825716858873	-0.0554970596119	3.21188745546	1.18064013789	0.497581886954	0.0538696250074	-0.111345679345	0.00710968063402	-0.210367415275	-0.139987766026	0.343488418438	-0.0829633654511	-0.0840364029269	0.0684149052933	0.309399132729	0.0867409697787	-0.0255179887197	0.323111233964	0.00907712716687	0.21683941133	-7.24105807196	7.65669249924	-0.922973231354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 90 through 96 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 97 through 110 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 141 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 142 through 152 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 153 through 177 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 178 through 202 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 203 through 221 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 222 through 232 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 88 through 110 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 111 through 124 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 125 through 134 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 135 through 153 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 154 through 187 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 193 through 216 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 217 through 232 )

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