PDB-5iw9: Structure of bacteriophage T4 gp25, sheath polymerization initiator

ID or keywords:

Entry

Database: PDB / ID: 5iw9

Title

Structure of bacteriophage T4 gp25, sheath polymerization initiator

Components

Baseplate wedge protein gp25

Keywords

VIRAL PROTEIN / contractile sheath /

baseplate / wedge / sheath polymerization

Function / homology

IraD/Gp25-like / Baseplate wedge protein gp25 / virus tail, baseplate / Nuclear Transport Factor 2; Chain: A, - #40 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Baseplate wedge protein gp25

Function and homology information

Biological species

Enterobacteria phage T4 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.47 Å

Authors

Leiman, P.G. / Browning, C. / Shneider, M.M.

Funding support

Switzerland, 1items

Citation

Journal: Nature / Year: 2016
Title: Structure of the T4 baseplate and its function in triggering sheath contraction.
Authors: Nicholas M I Taylor / Nikolai S Prokhorov / Ricardo C Guerrero-Ferreira / Mikhail M Shneider / Christopher Browning / Kenneth N Goldie / Henning Stahlberg / Petr G Leiman /

Abstract: Several systems, including contractile tail bacteriophages, the type VI secretion system and R-type pyocins, use a multiprotein tubular apparatus to attach to and penetrate host cell membranes. This ...

History

Deposition	Mar 22, 2016	Deposition site: RCSB / Processing site: PDBE
Supersession	May 11, 2016	ID: 4HRZ
Revision 1.0	May 11, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 25, 2016	Group: Database references
Revision 1.2	Jun 8, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5iw9.cif.gz	116.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5iw9.ent.gz	98.1 KB	Display	PDB format
PDBx/mmJSON format	5iw9.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/iw/5iw9 ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iw9	HTTPS FTP

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Related structure data

Related structure data	3374C 3392C 3393C 3394C 3395C 3396C 3397C 5iv5C 5iv7C C: citing same article (ref.)
Similar structure data	6cds-1 6y9m-1 6y9l-2 6cds-2 5fuc-1 4qdy-1 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: Baseplate wedge protein gp25

B: Baseplate wedge protein gp25

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	69.859, 69.859, 222.179
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Components on special symmetry positions

ID	Model	Components
1	1	B-242- HOH
2	1	B-259- HOH

#1: Protein	Baseplate wedge protein gp25 / Outer wedge of baseplate protein / Protein Gp25 Mass: 15120.591 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 25 / Plasmid: pTSL / Details (production host): pet-28 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): 834 / Variant (production host): DE3 / References: UniProt: P09425
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Baseplate wedge protein gp25 / Outer wedge of baseplate protein / Protein Gp25

Mass: 15120.591 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacteria phage T4 (virus) / Gene: 25 / Plasmid: pTSL / Details (production host): pet-28 derivative / Production host:

Escherichia coli (E. coli) / Strain (production host): 834 / Variant (production host): DE3 / References: UniProt: P09425

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.65 Å³/Da / Density % sol: 73.53 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.9M-1.0M MG2SO4, 0.1M MES pH 6.2, protein concentration = 20 mg/ml

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 0.9793 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2009 / Details: DYNAMICALLY BENDABLE MIRROR

Radiation

Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2.47→74.06 Å / Num. obs: 20716 / % possible obs: 100 % / Redundancy: 23.4 % / B_iso Wilson estimate: 51.75 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.085 / Net I/av σ(I): 30.8 / Net I/σ(I): 30.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.47-2.57	24.8	0.843	5.2	1	100
8.91-74.06	19.1	0.043		1	99.5

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2328: ???)	refinement
SCALA	0.5.23	data scaling
PDB_EXTRACT	3.2	data extraction
iMOSFLM	7.2.1	data reduction
SHELXCD	2006/3	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.47→69.86 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 20.17 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2172	1774	4.71 %	random
R_work	0.1898	-	-	-
obs	0.1911	20649	99.93 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.47→69.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2016	0	0	104	2120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2066
X-RAY DIFFRACTION	f_angle_d	0.506	2805
X-RAY DIFFRACTION	f_dihedral_angle_d	16.598	1299
X-RAY DIFFRACTION	f_chiral_restr	0.045	323
X-RAY DIFFRACTION	f_plane_restr	0.004	369

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 (%)
2.4702-2.537	0.262	124	0.2423	2739	X-RAY DIFFRACTION	100
2.537-2.6116	0.2553	135	0.2379	2777	X-RAY DIFFRACTION	100
2.6116-2.6959	0.2559	145	0.2281	2776	X-RAY DIFFRACTION	100
2.6959-2.7923	0.266	175	0.2274	2737	X-RAY DIFFRACTION	100
2.7923-2.9041	0.2523	131	0.2239	2747	X-RAY DIFFRACTION	100
2.9041-3.0363	0.2807	131	0.2202	2755	X-RAY DIFFRACTION	100
3.0363-3.1964	0.2107	120	0.2215	2800	X-RAY DIFFRACTION	100
3.1964-3.3966	0.2365	151	0.1985	2732	X-RAY DIFFRACTION	100
3.3966-3.6589	0.2294	128	0.1959	2756	X-RAY DIFFRACTION	100
3.6589-4.027	0.2018	146	0.1641	2744	X-RAY DIFFRACTION	100
4.027-4.6097	0.1836	141	0.1488	2770	X-RAY DIFFRACTION	100
4.6097-5.8072	0.1953	119	0.165	2793	X-RAY DIFFRACTION	100
5.8072-69.8874	0.2047	128	0.1978	2749	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	3.9819	-0.4388	-3.9631	2.6991	1.9857	5.2583	0.9475	2.7622	-0.6328	-1.5357	-1.4159	-0.069	0.888	-0.4851	-0.3481	1.5488	0.1575	-0.1735	1.5442	-0.0445	1.1274	2.2695	-41.5586	26.0835
2	0.2089	1.3255	0.0348	4.9577	-0.8847	3.8646	0.2963	0.3335	0.4851	0.1479	0.1549	0.7243	-0.2436	-0.9233	-0.1305	0.4302	0.0419	0.0674	0.6039	0.0302	0.3815	19.519	-19.1113	22.4964
3	3.7653	-3.6695	-3.3323	6.5525	3.4825	3.3216	0.6034	-0.1437	0.9797	-0.3037	0.2891	-0.4277	-0.8313	0.7364	-0.8196	0.5513	-0.1289	0.1053	0.6364	-0.0069	0.5851	44.5711	-9.63	13.3037
4	1.8727	2.1936	-1.2262	3.0892	-2.4236	4.3291	0.0221	-0.1945	-0.0887	0.637	0.5151	-1.4256	-0.1897	0.6077	-0.5806	1.2091	-0.1337	0.3188	0.8706	-0.2537	1.3281	44.294	8.1572	19.4004
5	3.2172	2.3392	0.5301	7.8304	4.3881	3.6482	0.1403	0.3251	0.8233	-0.2983	0.3775	0.1142	-0.6486	-0.1139	-0.3978	0.6412	0.0504	0.1466	0.3824	0.1297	0.5797	32.3519	0.7113	17.1818
6	3.9249	-0.8491	-3.8213	5.212	4.5823	6.7399	0.3054	1.6481	-0.5836	-1.0491	-0.9033	1.0128	0.2179	-2.7466	0.6213	0.636	0.1539	0.0355	0.8773	0.0568	0.6511	17.3252	-9.9541	15.9048
7	5.7055	4.9946	5.4683	4.518	5.1772	7.2017	0.8026	-1.1775	1.4001	0.8435	-0.6167	0.9808	-0.5551	-0.8032	0.0366	0.7713	0.0558	0.1355	0.4333	0.0236	0.6682	32.2912	-1.2829	25.3703
8	3.1265	3.915	-3.6318	5.17	-4.6202	4.2195	-0.2946	-0.4585	-2.3776	0.1551	-3.0758	1.5254	-0.9089	0.4684	3.5346	1.4528	-0.1284	0.0267	1.4538	0.0993	1.5095	17.4327	-19.7285	-18.063
9	4.1319	-1.3435	-2.3835	3.843	-2.5798	4.5727	-0.4173	0.1978	-1.268	0.5459	0.2894	1.5536	0.9998	-1.0708	-0.1327	0.6179	-0.0089	0.0568	0.9486	-0.1218	0.9211	21.6159	-22.5286	-9.4375
10	7.0706	-2.889	4.0534	3.7109	-2.816	3.3066	0.2662	0.0984	-0.3457	-0.2212	-0.0476	-0.0197	0.0942	-0.3398	-0.3219	0.361	-0.0291	0.0395	0.3825	0.0473	0.288	35.3724	-19.1071	10.3358
11	3.6187	-3.2628	-4.0864	3.4711	4.136	5.2796	-0.2954	-1.2246	-0.361	1.079	0.5389	-0.0938	0.3743	0.6083	-0.2832	0.6318	-0.0364	0.0171	0.6842	0.0254	0.429	36.6481	-16.515	30.6145
12	9.6515	-2.7982	0.4215	9.4274	0.3064	2.2546	-0.2461	-3.5899	0.5255	0.9642	-0.2016	-0.6617	-2.3357	-0.9698	0.4018	0.8329	-0.0576	-0.1934	1.3911	0.1686	0.8926	49.7339	-24.818	33.1823
13	9.2668	-2.8938	3.5206	4.9436	-2.9258	5.2999	0.2732	-0.6861	-1.1048	0.2179	-0.1226	-0.0925	0.2241	0.2686	-0.1082	0.3926	-0.0922	-0.0249	0.5525	0.1883	0.5024	37.8415	-29.4366	24.8521
14	4.0484	-4.0968	4.2811	5.5133	-1.9292	8.3312	0.2519	0.5874	-0.6034	-0.1514	-0.3679	-0.6818	0.1823	1.028	0.1966	0.4157	-0.0514	-0.0343	0.5436	0.1899	0.6074	47.4839	-31.2336	21.0268
15	3.3657	-4.8294	-4.0269	7.0366	5.6603	4.9085	0.7233	2.8901	-3.0138	-1.3927	-1.0415	1.9944	-0.526	-1.4644	0.3313	0.6341	-0.043	-0.0413	0.8858	-0.2354	0.8614	29.3996	-29.2018	7.5576
16	6.629	1.2064	8.0822	9.2673	1.8812	9.9968	0.614	0.9514	0.0469	0.2596	-0.831	-0.7039	0.5812	1.5573	0.025	0.3173	-0.1223	0.0129	0.6706	0.1033	0.5802	46.8637	-25.0539	18.0085

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 56 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 57 through 68 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 69 through 110 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 111 through 119 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 120 through 128 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 5 through 12 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 13 through 20 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 21 through 41 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 42 through 56 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 57 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 90 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 91 through 110 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 111 through 119 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 120 through 129 )

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