PDB-4jmq: Crystal structure of pb9: The Dit of bacteriophage T5.

ID or keywords:

Entry

Database: PDB / ID: 4jmq

Title

Crystal structure of pb9: The Dit of bacteriophage T5.

Components

Bacteriophage T5 distal tail protein

Keywords

VIRAL PROTEIN / distal tail protein / E. coli infecting T5 bacteriophage / Siphoviridae family

Function / homology

Function and homology information

virus tail, baseplate / virus tail
Similarity search - Function

Biological species

Enterobacteria phage T5 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.895 Å

Authors

Flayhan, A. / Vellieux, F.M.D. / Girard, E. / Maury, O. / Boulanger, P. / Breyton, C.

Citation

Journal: J.Virol. / Year: 2014
Title: Crystal Structure of pb9, the Distal Tail Protein of Bacteriophage T5: a Conserved Structural Motif among All Siphophages.
Authors: Flayhan, A. / Vellieux, F.M. / Lurz, R. / Maury, O. / Contreras-Martel, C. / Girard, E. / Boulanger, P. / Breyton, C.

History

Deposition	Mar 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2013	Group: Database references
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4jmq.cif.gz	332.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4jmq.ent.gz	273.5 KB	Display	PDB format
PDBx/mmJSON format	4jmq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4jmq_validation.pdf.gz	450.8 KB	Display	wwPDB validaton report
Full document	4jmq_full_validation.pdf.gz	459.1 KB	Display
Data in XML	4jmq_validation.xml.gz	38.9 KB	Display
Data in CIF	4jmq_validation.cif.gz	57 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/4jmq ftp://data.pdbj.org/pub/pdb/validation_reports/jm/4jmq	HTTPS FTP

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Related structure data

Similar structure data	5mf2-4 5wi2-d 4pcw-1 4g50-2 6o4a-1 5mf2-1 5mf2-3 5v8t-2 3vaw-d 3wwq-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bacteriophage T5 distal tail protein

B: Bacteriophage T5 distal tail protein

C: Bacteriophage T5 distal tail protein

D: Bacteriophage T5 distal tail protein

97.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacteriophage T5 distal tail protein

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

2

B: Bacteriophage T5 distal tail protein

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

3

C: Bacteriophage T5 distal tail protein

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

4

D: Bacteriophage T5 distal tail protein

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

Unit cell

Length a, b, c (Å)	55.657, 70.027, 71.014
Angle α, β, γ (deg.)	91.05, 107.66, 112.03
Int Tables number	1
Space group name H-M	P1

#1: Protein	Bacteriophage T5 distal tail protein / Tail protein pb9 Mass: 24479.426 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T5 (virus) / Gene: T5.139, T5p135 / Plasmid: pLIM13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QGE8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 829 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Bacteriophage T5 distal tail protein / Tail protein pb9

Mass: 24479.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacteria phage T5 (virus) / Gene: T5.139, T5p135 / Plasmid: pLIM13 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6QGE8

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.47 Å³/Da / Density % sol: 50.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10 to 14% (w/v) PEG 3350, 0.05M MES, 0.1 to 0.2M MgCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 173 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2011
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.89→27.689 Å / Num. all: 209072 / Num. obs: 70953 / % possible obs: 95.38 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 1.09 / Redundancy: 2.94 % / B_iso Wilson estimate: 38.27 Å² / R_merge(I) obs: 0.159 / R_sym value: 0.194 / Net I/σ(I): 6.38

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SAD
Starting model: Poly-Ala model

Resolution: 1.895→27.689 Å / SU ML: 0.3 / σ(F): 1.99 / Phase error: 27.6 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2518	3548	5 %	RANDOM
R_work	0.2029	-	-	-
obs	0.2053	70953	95.38 %	-
all	-	209072	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.895→27.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6080	0	0	829	6909

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6265
X-RAY DIFFRACTION	f_angle_d	1.139	8524
X-RAY DIFFRACTION	f_dihedral_angle_d	13.046	2297
X-RAY DIFFRACTION	f_chiral_restr	0.073	930
X-RAY DIFFRACTION	f_plane_restr	0.006	1109

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 (%)
1.8949-1.9208	0.4078	88	0.35	1677	X-RAY DIFFRACTION	59
1.9208-1.9482	0.375	142	0.3313	2698	X-RAY DIFFRACTION	95
1.9482-1.9773	0.3815	141	0.303	2678	X-RAY DIFFRACTION	95
1.9773-2.0082	0.3522	140	0.3018	2650	X-RAY DIFFRACTION	95
2.0082-2.0411	0.3163	143	0.2825	2727	X-RAY DIFFRACTION	96
2.0411-2.0763	0.3099	141	0.2717	2677	X-RAY DIFFRACTION	96
2.0763-2.114	0.3487	143	0.2512	2719	X-RAY DIFFRACTION	96
2.114-2.1547	0.3023	145	0.2427	2754	X-RAY DIFFRACTION	96
2.1547-2.1986	0.3013	143	0.2258	2711	X-RAY DIFFRACTION	97
2.1986-2.2464	0.2528	146	0.2155	2770	X-RAY DIFFRACTION	97
2.2464-2.2987	0.2766	145	0.2248	2766	X-RAY DIFFRACTION	97
2.2987-2.3561	0.3163	141	0.2191	2681	X-RAY DIFFRACTION	97
2.3561-2.4198	0.277	146	0.2061	2778	X-RAY DIFFRACTION	97
2.4198-2.491	0.2687	145	0.2129	2744	X-RAY DIFFRACTION	97
2.491-2.5713	0.2737	143	0.209	2725	X-RAY DIFFRACTION	98
2.5713-2.6631	0.2786	146	0.2054	2775	X-RAY DIFFRACTION	97
2.6631-2.7697	0.2571	146	0.1991	2770	X-RAY DIFFRACTION	98
2.7697-2.8956	0.2395	145	0.1926	2755	X-RAY DIFFRACTION	98
2.8956-3.0481	0.2357	146	0.1884	2762	X-RAY DIFFRACTION	98
3.0481-3.2388	0.212	147	0.1765	2797	X-RAY DIFFRACTION	98
3.2388-3.4884	0.2566	145	0.174	2765	X-RAY DIFFRACTION	98
3.4884-3.8386	0.1728	145	0.16	2748	X-RAY DIFFRACTION	98
3.8386-4.3922	0.1918	145	0.1576	2752	X-RAY DIFFRACTION	98
4.3922-5.5265	0.2024	146	0.1603	2779	X-RAY DIFFRACTION	98
5.5265-27.6921	0.2281	145	0.2095	2747	X-RAY DIFFRACTION	97

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	3.9001	-2.6642	-3.1193	3.6809	1.5342	5.6744	0.1981	0.0078	0.0954	-0.156	-0.0861	0.1242	-0.0793	-0.1835	-0.0585	0.344	-0.0255	0.0367	0.1632	-0.0007	0.2451	-27.7995	31.278	44.0623
2	5.4413	1.0219	0.7221	3.6756	1.7469	6.1932	-0.2546	-0.1729	-0.4934	-0.4299	0.2645	-0.0634	0.5076	0.337	-0.0455	0.3839	0.0336	0.0434	0.1425	0.0547	0.2361	-19.8234	24.9603	38.6221
3	6.2058	2.3271	-1.9483	6.9788	0.5554	8.6556	-0.2845	0.3163	-0.3578	-0.4604	-0.0126	0.286	0.2195	-0.8068	0.2553	0.1998	0.0566	-0.0011	0.2665	0.0073	0.2653	-34.5986	25.3375	44.4186
4	2.4191	-0.8175	-1.6901	5.4002	-0.9065	9.1857	0.2176	-0.019	0.1015	0.0807	0.0385	0.1379	-0.3411	-0.5421	-0.1976	0.2516	-0.0817	0.0202	0.2931	-0.0045	0.2104	-20.7453	44.5252	24.9925
5	1.0779	1.5376	-1.7539	2.8299	-3.4141	4.2555	0.1061	0.0479	0.0471	0.0937	-0.0294	0.1023	-0.0163	-0.0117	-0.0637	0.3194	0.0246	0.0276	0.2525	0.007	0.1958	-20.9333	35.5405	30.6531
6	6.2617	0.6179	-0.7005	4.0235	-1.4217	2.5302	-0.3663	0.0895	-0.2525	0.1944	-0.1153	-0.1007	1.6137	0.237	0.498	0.2835	-0.0356	0.0169	0.1544	0.0327	0.2327	-27.5887	22.9951	46.7255
7	6.3663	-0.2491	2.7891	1.3341	-0.0803	3.2116	0.0336	-0.0667	0.0991	0.0287	0.1241	0.0456	-0.0059	0.0329	-0.1884	0.345	-0.0043	0.0491	0.1721	-0.0051	0.2311	-14.9164	14.2435	57.056
8	7.476	5.4932	0.0418	6.8444	0.3514	2.0289	-0.1004	0.2899	0.2635	-0.1161	0.2402	-0.0498	0.2521	0.005	-0.1366	0.3254	0.0443	-0.0003	0.1521	0.0402	0.1646	-14.2448	15.9724	50.3288
9	8.1125	1.9321	-6.2498	5.8704	-2.1267	5.4082	-0.1437	0.1205	-0.3929	-0.166	-0.2416	-0.1905	0.5531	-0.0917	0.4427	0.3357	0.0298	-0.0668	0.2669	-0.0028	0.3568	-15.1674	8.4519	53.1976
10	6.2475	2.7794	3.4766	3.6855	3.3001	4.0513	-0.1018	0.1344	0.0365	-0.022	0.0094	-0.3092	0.1508	0.2938	-0.1183	0.359	-0.0542	0.064	0.2044	0.0249	0.2233	-23.5251	-7.3686	66.0593
11	1.1883	2.1195	-1.545	6.0085	-3.0486	2.0201	-0.0004	-0.0429	-0.0453	0.0948	-0.07	-0.0425	-0.0193	0.0733	0.0659	0.2577	0.0021	0.0133	0.1853	-0.0038	0.2034	-24.0541	-0.1729	60.0708
12	7.0783	3.2903	0.6653	2.6859	0.9805	3.8125	-0.0167	0.2286	0.2487	-0.1002	0.0565	0.1148	-0.2053	-0.0662	0.0235	0.3009	0.0415	0.0436	0.185	0.0253	0.2032	-16.4153	18.8894	49.3449
13	3.8739	-0.6394	4.9918	1.5824	-0.5443	5.8006	0.387	-0.0625	-0.2054	-0.382	-0.2563	-0.061	0.425	0.1377	-0.3395	0.4749	0.049	0.0641	0.3325	0.032	0.2295	-24.4545	52.0379	53.0668
14	0.2173	-0.2985	-0.1388	2.8972	-0.3994	5.0634	0.0354	0.1822	0.1274	-0.6617	-0.1385	-0.2047	-0.1202	0.0338	0.0823	0.3553	0.0297	0.0739	0.2239	0.0166	0.2786	-24.0306	58.8205	53.5562
15	2.2619	1.1499	-0.7707	3.095	-0.7561	2.8749	0.032	0.08	0.1958	-0.0921	0.0055	0.0221	-0.1028	-0.1074	-0.0442	0.2706	0.0336	0.0296	0.1757	0.0026	0.1853	-30.398	44.8398	69.9599
16	2.7203	-1.0515	1.6907	6.4906	0.2521	2.7373	-0.3152	-0.2409	0.1904	0.1225	0.1153	-0.0666	0.1116	0.0703	0.1358	0.2983	-0.0467	-0.001	0.1888	0.1122	0.3962	-24.1869	63.3924	56.8563
17	3.7345	-2.5518	-0.9869	4.55	3.3891	4.7369	0.5369	-0.0688	-0.2256	-0.4933	-0.0295	-0.3218	0.2102	0.0148	-0.4629	0.4808	-0.0741	-0.0244	0.2408	0.068	0.3273	-15.0994	18.8083	79.1688
18	1.4943	-0.4573	-0.1814	5.4093	-1.7637	2.0649	0.0211	-0.2269	-0.2677	0.9901	0.2866	-0.2056	0.2707	-0.0958	-0.276	0.6861	-0.0401	-0.0887	0.3234	0.0269	0.3186	-15.2177	18.0841	87.288
19	7.1279	2.301	-5.0455	2.2631	-1.3642	6.6407	0.0176	-0.221	-0.4387	-0.5887	0.0129	-0.1497	0.1972	-0.1565	-0.0222	0.4598	0.0055	-0.0552	0.1933	0.0281	0.3886	-9.8836	26.625	71.2862
20	3.161	1.1551	-1.2505	3.0199	-0.8031	2.9523	0.0594	-0.0657	0.0089	0.1601	-0.0453	-0.1473	-0.0149	0.0215	-0.018	0.2738	0.0183	-0.0199	0.1411	-0.0076	0.2001	-5.8784	39.8725	72.5462
21	2.0203	-0.3645	-1.2598	3.6941	-0.5229	1.207	0.2606	-1.2246	-0.7378	0.7054	-0.3738	0.4353	0.6911	-0.6408	0.1298	0.913	-0.2814	-0.0025	0.5364	0.2872	0.5543	-20.4483	16.6402	88.0988

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:27 )	A	1 - 27
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 43:55 )	A	43 - 55
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 56:85 )	A	56 - 85
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 86:115 )	A	86 - 115
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 116:188 )	A	116 - 188
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 189:205 )	A	189 - 205
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 1:26 )	B	1 - 26
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 43:72 )	B	43 - 72
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 73:88 )	B	73 - 88
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 89:108 )	B	89 - 108
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 109:188 )	B	109 - 188
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 189:205 )	B	189 - 205
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 1:26 )	C	1 - 26
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 45:85 )	C	45 - 85
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 86:186 )	C	86 - 186
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 187:217 )	C	187 - 217
17	X-RAY DIFFRACTION	17	( CHAIN D AND RESID 1:26 )	D	1 - 26
18	X-RAY DIFFRACTION	18	( CHAIN D AND RESID 43:78 )	D	43 - 78
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 79:94 )	D	79 - 94
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 95:173 )	D	95 - 173
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 174:204 )	D	174 - 204

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Yorodumi