PDB-5fhy: Crystal structure of FliD (HAP2) from Pseudomonas aeruginosa PAO1

ID or keywords:

Entry

Database: PDB / ID: 5fhy

Title

Crystal structure of FliD (HAP2) from Pseudomonas aeruginosa PAO1

Components

B-type flagellar hook-associated protein 2

Keywords

STRUCTURAL PROTEIN / bacterial flagella / 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

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.201 Å

Authors

Postel, S. / Bonsor, D. / Diederichs, K. / Sundberg, E.J.

Citation

Journal: Elife / Year: 2016
Title: Bacterial flagellar capping proteins adopt diverse oligomeric states.
Authors: Postel, S. / Deredge, D. / Bonsor, D.A. / Yu, X. / Diederichs, K. / Helmsing, S. / Vromen, A. / Friedler, A. / Hust, M. / Egelman, E.H. / Beckett, D. / Wintrode, P.L. / Sundberg, E.J.

History

Deposition	Dec 22, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5fhy.cif.gz	182.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5fhy.ent.gz	144.3 KB	Display	PDB format
PDBx/mmJSON format	5fhy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fhy_validation.pdf.gz	445.4 KB	Display	wwPDB validaton report
Full document	5fhy_full_validation.pdf.gz	449.9 KB	Display
Data in XML	5fhy_validation.xml.gz	18.4 KB	Display
Data in CIF	5fhy_validation.cif.gz	25.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/5fhy ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fhy	HTTPS FTP

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Related structure data

Similar structure data	20608 5e7o-d 20150 22048 22049 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: B-type flagellar hook-associated protein 2

B: B-type flagellar hook-associated protein 2

hetero molecules

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

1

B: B-type flagellar hook-associated protein 2

hetero molecules

x 6

A: B-type flagellar hook-associated protein 2

hetero molecules

x 6

defined by author&software
431 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_765	-y+2,x-y+1,z	1
crystal symmetry operation	3_675	-x+y+1,-x+2,z	1
crystal symmetry operation	4_775	-x+2,-y+2,z	1
crystal symmetry operation	5_565	y,-x+y+1,z	1
crystal symmetry operation	6_655	x-y+1,x,z	1
crystal symmetry operation	1_554	x,y,z-1	1
crystal symmetry operation	2_764	-y+2,x-y+1,z-1	1
crystal symmetry operation	3_674	-x+y+1,-x+2,z-1	1
crystal symmetry operation	4_774	-x+2,-y+2,z-1	1
crystal symmetry operation	5_564	y,-x+y+1,z-1	1
crystal symmetry operation	6_654	x-y+1,x,z-1	1

2

A: B-type flagellar hook-associated protein 2

B: B-type flagellar hook-associated protein 2

hetero molecules

x 6

defined by software
431 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_765	-y+2,x-y+1,z	1
crystal symmetry operation	3_675	-x+y+1,-x+2,z	1
crystal symmetry operation	4_775	-x+2,-y+2,z	1
crystal symmetry operation	5_565	y,-x+y+1,z	1
crystal symmetry operation	6_655	x-y+1,x,z	1

Unit cell

Length a, b, c (Å)	124.741, 124.741, 107.010
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	168
Space group name H-M	P6

#1: Protein	B-type flagellar hook-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein Mass: 35875.734 Da / Num. of mol.: 2 / Fragment: UNP residues 78-405 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria) Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: fliD, PA1094 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: Q9K3C5
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.35 Å³/Da / Density % sol: 63.28 % / Description: hexagonal thick plates
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystallized in 0.8 M NaK Tartrate, 0.1 M Hepes pH 7.5 using random matrix microseed screening Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2015
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.2→62.4 Å / Num. all: 367311 / Num. obs: 47974 / % possible obs: 99.9 % / Redundancy: 7.7 % / B_iso Wilson estimate: 60.67 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 17.15
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 7.5 % / R_merge(I) obs: 3.702 / Mean I/σ(I) obs: 0.55 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: low resolution SeMet protein

Resolution: 2.201→62.371 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 38.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2867	4594	4.92 %	random
R_work	0.2492	-	-	-
obs	0.251	47968	98.76 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.201→62.371 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3128	0	3	88	3219

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3149
X-RAY DIFFRACTION	f_angle_d	0.955	4287
X-RAY DIFFRACTION	f_dihedral_angle_d	11.284	1077
X-RAY DIFFRACTION	f_chiral_restr	0.033	551
X-RAY DIFFRACTION	f_plane_restr	0.003	561

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 (%)
2.2006-2.2257	0.4592	138	0.4097	2919	X-RAY DIFFRACTION	94
2.2257-2.2518	0.3855	153	0.4221	2908	X-RAY DIFFRACTION	98
2.2518-2.2793	0.4014	151	0.4137	2937	X-RAY DIFFRACTION	98
2.2793-2.3082	0.4165	158	0.4055	2927	X-RAY DIFFRACTION	99
2.3082-2.3385	0.3944	151	0.404	2977	X-RAY DIFFRACTION	98
2.3385-2.3706	0.4395	161	0.3901	2910	X-RAY DIFFRACTION	99
2.3706-2.4044	0.3864	151	0.3762	2952	X-RAY DIFFRACTION	99
2.4044-2.4403	0.37	170	0.3665	2921	X-RAY DIFFRACTION	98
2.4403-2.4785	0.4205	158	0.3651	2983	X-RAY DIFFRACTION	99
2.4785-2.5191	0.3732	127	0.3472	2921	X-RAY DIFFRACTION	99
2.5191-2.5625	0.3745	159	0.3544	3000	X-RAY DIFFRACTION	99
2.5625-2.6091	0.3517	142	0.3512	2999	X-RAY DIFFRACTION	99
2.6091-2.6593	0.3574	180	0.3335	2885	X-RAY DIFFRACTION	99
2.6593-2.7136	0.363	147	0.3427	2981	X-RAY DIFFRACTION	99
2.7136-2.7726	0.3759	155	0.329	2995	X-RAY DIFFRACTION	99
2.7726-2.8371	0.3759	132	0.3236	2972	X-RAY DIFFRACTION	99
2.8371-2.908	0.3302	144	0.3173	2959	X-RAY DIFFRACTION	99
2.908-2.9867	0.3076	175	0.2847	2933	X-RAY DIFFRACTION	99
2.9867-3.0745	0.3331	160	0.2778	2934	X-RAY DIFFRACTION	99
3.0745-3.1738	0.3086	149	0.2694	3011	X-RAY DIFFRACTION	99
3.1738-3.2872	0.3195	164	0.2637	2938	X-RAY DIFFRACTION	99
3.2872-3.4188	0.3043	132	0.2592	2988	X-RAY DIFFRACTION	99
3.4188-3.5744	0.306	144	0.2481	3011	X-RAY DIFFRACTION	99
3.5744-3.7628	0.3131	192	0.234	2904	X-RAY DIFFRACTION	99
3.7628-3.9985	0.269	172	0.2331	2981	X-RAY DIFFRACTION	99
3.9985-4.3072	0.2138	157	0.1995	2977	X-RAY DIFFRACTION	99
4.3072-4.7405	0.233	141	0.1875	2980	X-RAY DIFFRACTION	100
4.7405-5.4261	0.2603	138	0.2061	3009	X-RAY DIFFRACTION	100
5.4261-6.835	0.2233	166	0.2243	2974	X-RAY DIFFRACTION	100
6.835-62.3955	0.2429	127	0.208	3025	X-RAY DIFFRACTION	99

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	7.4424	6.0343	-1.2688	8.2976	-1.6742	1.9145	0.5859	-0.9005	-0.02	0.945	-0.893	-0.2957	0.045	0.1793	0.2204	0.4121	-0.06	-0.1358	0.4917	0.001	0.406	38.2286	132.1521	74.294
2	5.0713	-3.7484	-2.3077	7.873	2.0635	3.441	0.3618	-0.4016	0.4515	0.1167	-0.2643	0.005	-0.5329	0.0212	-0.098	0.5423	-0.0079	-0.1488	0.5557	-0.0898	0.8827	56.455	161.7292	72.6929
3	6.7984	4.5337	1.083	6.9736	-0.1619	5.4146	-0.5148	0.4976	1.7714	-1.0236	0.53	1.0227	-0.5031	-0.1099	-0.0238	0.5381	0.0161	-0.1656	0.5993	0.1235	1.0676	51.2266	161.4343	65.6534
4	6.2696	3.1092	0.6146	4.4665	-0.1956	0.5212	-0.1357	0.1826	0.3386	-0.2161	-0.1204	0.2791	-0.1456	0.0591	0.1613	0.4031	-0.0045	-0.1552	0.4552	0.0066	0.3803	41.466	137.8095	68.4069
5	4.9568	-0.4486	-6.7861	-0.0264	0.5265	9.2161	-0.5512	-0.6508	-0.455	0.832	-0.2807	0.3947	3.2503	0.1625	0.8493	1.4907	-0.4466	0.043	0.8484	0.1687	0.6019	27.8606	120.0644	98.0901
6	7.0124	7.4786	6.9114	7.966	7.3654	6.808	-2.0087	-0.1935	1.0446	-2.3674	0.8612	0.2189	-2.4983	1.0742	0.5544	1.9576	0.0661	0.4447	1.6916	0.1765	0.4362	29.1673	119.5451	130.2256
7	7.2656	-3.5441	0.6166	4.154	1.6383	1.5871	-0.1841	0.9023	0.102	-0.1146	0.4753	-0.1515	0.382	-0.1236	-0.3228	0.9811	-0.0973	-0.1139	0.8722	0.0908	0.549	80.5687	136.9242	37.5367
8	4.6776	0.5448	-0.3794	2.3967	1.363	4.8623	-0.1297	0.3583	0.6796	-0.161	0.1063	0.2399	-0.7323	-0.3986	0.0417	0.8257	0.1049	-0.1152	0.7858	0.2594	0.7819	57.6323	161.8827	41.1524
9	8.7509	-3.4701	-0.6507	2.1358	0.2037	0.9478	0.331	0.8197	0.2721	-0.6052	-0.1809	0.0656	0.0581	-0.0753	-0.1825	1.0742	-0.1817	-0.1322	0.8049	0.1275	0.5427	77.029	140.5169	42.7611
10	0.9767	1.4202	-0.4564	1.7621	-0.6712	0.4924	-0.1901	-1.041	-0.4294	0.6848	0.1016	-0.6561	-0.8967	-0.6672	0.1202	1.5963	0.2396	-0.0583	1.2946	-0.0885	0.6744	94.5681	126.5426	-2.0341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 80 through 109 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 110 through 180 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 181 through 212 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 213 through 268 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 269 through 296 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 297 through 308 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 80 through 109 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 110 through 212 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 213 through 273 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 274 through 308 )

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