PDB-5fb4: Crystal structure of the bacteriophage phi29 tail knob protein gp...

ID or keywords:

Entry

Database: PDB / ID: 5fb4

Title

Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant

Components

Distal tube protein

Keywords

VIRAL PROTEIN / bacteriophage phi29 / tail knob

Function / homology

Function and homology information

virus tail, tube / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane
Similarity search - Function

Biological species

Bacillus phage phi29 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.039 Å

Authors

Xu, J.W. / Gui, M. / Wang, D.H. / Xiang, Y.

Funding support

China, 4items

Organization	Grant number	Country
973 program	2015CB13910102	China
the National Natural Science Foundation of China	31470721	China
Science Foundation of China	81550001	China
the Junior Thousand Talents Program of China	201311770418	China

Citation

Journal: Nature / Year: 2016
Title: The bacteriophage ϕ29 tail possesses a pore-forming loop for cell membrane penetration.
Authors: Jingwei Xu / Miao Gui / Dianhong Wang / Ye Xiang /

Abstract: Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine ...

History

Deposition	Dec 14, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jun 22, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5fb4.cif.gz	648.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5fb4.ent.gz	533.2 KB	Display	PDB format
PDBx/mmJSON format	5fb4.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/fb/5fb4 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fb4	HTTPS FTP

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Related structure data

Related structure data	6556C 6557C 6558C 5fb5C 5feiSC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5fei-1 4ep0-1 4eo2-d 4ep0-2 3ooh-d 20509 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: Distal tube protein

B: Distal tube protein

C: Distal tube protein

hetero molecules

206 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Distal tube protein

B: Distal tube protein

C: Distal tube protein

hetero molecules

A: Distal tube protein

B: Distal tube protein

C: Distal tube protein

hetero molecules

defined by author&software
411 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.600, 135.161, 313.431
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Distal tube protein / Gene product 9 / gp9 Mass: 68400.758 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04331
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1312 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE EXPERIMENTAL INFO OF UNIPROT (P04331, TUB9_BPPH2) REPORTS CONFLICT AT THESE POSITIONS 21 AND ...THE EXPERIMENTAL INFO OF UNIPROT (P04331, TUB9_BPPH2) REPORTS CONFLICT AT THESE POSITIONS 21 AND 141 (in Ref. 2; ACE96032).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.62 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.94% v/v ethanol, 10% PEG-400, HEPES buffer pH 7.5, magnesium chloride

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Data collection

Diffraction	Mean temperature: 160 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 3, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.039→43.32 Å / Num. obs: 126814 / % possible obs: 99.29 % / Redundancy: 6.1 % / Net I/σ(I): 17.66
Reflection shell	Redundancy: 5.9 % / Mean I/σ(I) obs: 9.2 / % possible all: 95.11

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data collection
HKL-2000		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FEI

5fei

Resolution: 2.039→43.317 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1832	6371	5.02 %
R_work	0.1531	-	-
obs	0.1547	126809	99.29 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.039→43.317 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12499	0	21	1312	13832

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12816
X-RAY DIFFRACTION	f_angle_d	1.053	17336
X-RAY DIFFRACTION	f_dihedral_angle_d	11.79	4709
X-RAY DIFFRACTION	f_chiral_restr	0.048	1843
X-RAY DIFFRACTION	f_plane_restr	0.005	2240

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 (%)
2.0392-2.0624	0.2087	198	0.1705	3389	X-RAY DIFFRACTION	85
2.0624-2.0867	0.1998	208	0.164	3986	X-RAY DIFFRACTION	100
2.0867-2.1121	0.1793	203	0.1584	4045	X-RAY DIFFRACTION	100
2.1121-2.1389	0.2108	236	0.1561	3954	X-RAY DIFFRACTION	100
2.1389-2.167	0.1961	229	0.1537	3986	X-RAY DIFFRACTION	100
2.167-2.1967	0.1918	206	0.1568	4001	X-RAY DIFFRACTION	100
2.1967-2.2281	0.1978	185	0.1575	4039	X-RAY DIFFRACTION	100
2.2281-2.2613	0.1836	205	0.1498	4034	X-RAY DIFFRACTION	100
2.2613-2.2966	0.1841	201	0.1514	4026	X-RAY DIFFRACTION	100
2.2966-2.3343	0.2048	202	0.1556	4004	X-RAY DIFFRACTION	100
2.3343-2.3745	0.1942	223	0.164	4011	X-RAY DIFFRACTION	100
2.3745-2.4177	0.2165	228	0.163	4006	X-RAY DIFFRACTION	100
2.4177-2.4642	0.2009	212	0.168	4017	X-RAY DIFFRACTION	100
2.4642-2.5145	0.2198	191	0.1671	4018	X-RAY DIFFRACTION	100
2.5145-2.5692	0.2273	187	0.1673	4072	X-RAY DIFFRACTION	100
2.5692-2.6289	0.228	228	0.1667	4001	X-RAY DIFFRACTION	100
2.6289-2.6947	0.2012	216	0.1637	4021	X-RAY DIFFRACTION	100
2.6947-2.7675	0.2193	191	0.166	4066	X-RAY DIFFRACTION	100
2.7675-2.8489	0.1845	213	0.1639	4030	X-RAY DIFFRACTION	100
2.8489-2.9409	0.1999	199	0.1626	4043	X-RAY DIFFRACTION	100
2.9409-3.046	0.2035	213	0.1639	4050	X-RAY DIFFRACTION	100
3.046-3.1679	0.1908	207	0.1585	4063	X-RAY DIFFRACTION	100
3.1679-3.312	0.1815	210	0.1481	4038	X-RAY DIFFRACTION	100
3.312-3.4866	0.1657	224	0.1486	4061	X-RAY DIFFRACTION	100
3.4866-3.7049	0.1483	228	0.1415	4036	X-RAY DIFFRACTION	100
3.7049-3.9908	0.1654	232	0.1333	4056	X-RAY DIFFRACTION	100
3.9908-4.392	0.1593	228	0.1304	4058	X-RAY DIFFRACTION	100
4.392-5.0267	0.1523	218	0.1281	4129	X-RAY DIFFRACTION	100
5.0267-6.33	0.1736	219	0.1582	4136	X-RAY DIFFRACTION	100
6.33-43.3272	0.1728	231	0.1717	4062	X-RAY DIFFRACTION	95

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	0.4241	-0.0313	0.1605	0.3149	0.2957	1.9209	-0.0572	-0.1416	0.0513	0.163	0.0364	-0.025	-0.0644	0.1047	0.0044	0.2021	0.0084	-0.014	0.1282	-0.0229	0.1869	94.1006	30.1694	100.8689
2	1.9801	-0.2591	-0.2645	1.3621	-0.1703	1.4218	0.0273	0.256	0.1328	-0.1471	0.006	0.021	-0.1023	0.0494	0.006	0.1625	-0.0183	-0.0122	0.1987	0.0468	0.1658	96.1814	33.504	18.9752
3	0.2554	-0.0255	-0.123	0.1323	-0.1644	1.4555	-0.0185	0.0263	0.0379	0.0108	0.014	0.0022	-0.0397	0.0265	0.0069	0.1128	-0.0109	-0.0157	0.0779	-0.0011	0.1641	95.7495	27.8825	61.1693
4	0.7367	-0.2031	0.6846	0.5916	-0.2638	1.6312	-0.1143	-0.3093	0.0761	0.3262	0.0419	-0.1063	-0.1407	-0.1775	-0.0159	0.2513	0.0198	-0.072	0.215	-0.0364	0.2321	121.1022	15.9926	100.8909
5	1.1734	-0.0543	-0.1441	2.031	0.0925	1.4524	0.0272	0.143	0.0188	-0.2009	-0.0007	-0.0862	0.0132	0.102	0.0133	0.1097	-0.0091	0.0117	0.2095	0.0222	0.1527	124.2382	15.1505	18.798
6	0.1798	-0.0307	-0.08	0.2468	0.1092	1.6294	-0.0086	0.0324	0.0232	0.0173	-0.0063	-0.0383	0.0132	-0.02	0.0158	0.0936	-0.0254	-0.0193	0.1133	0.0104	0.1828	119.1574	12.9686	60.215
7	0.4887	-0.0418	0.155	0.6647	-0.1666	0.4773	0.0734	-0.3148	-0.0327	0.5196	-0.2176	-0.3351	-0.2036	0.504	0.0351	0.3784	-0.0465	-0.1238	0.3838	0.0736	0.3005	125.6408	-16.6797	107.9861
8	0.5411	-0.0357	0.0656	1.0538	0.0435	0.5392	0.055	-0.4392	0.0131	0.9066	-0.2368	0.2408	-0.375	-0.0247	-0.0019	0.6824	-0.0549	-0.1034	0.3937	0.041	0.3825	120.8947	-13.7519	116.4817
9	0.3685	0.1247	-0.2622	0.7268	-0.6884	0.6216	0.0402	-0.0755	-0.0237	0.2343	-0.0535	-0.0549	-0.2114	0.16	-0.0107	0.1645	-0.0095	-0.0414	0.1052	-0.0019	0.1607	118.9008	-13.3467	88.5369
10	1.7056	0.4911	-0.0149	1.5802	0.1606	1.4476	-0.0513	0.2317	-0.0224	-0.2158	0.0142	-0.1047	0.076	0.0735	0.0183	0.1551	0.0155	0.0397	0.1915	-0.0006	0.1704	122.8479	-18.3027	18.9188
11	0.2192	0.0425	-0.1425	0.1968	0.0954	1.8364	-0.0104	0.0231	-0.0105	-0.0037	-0.0059	-0.0544	-0.0299	0.0339	0.021	0.0683	0.0204	-0.0029	0.1105	0.0062	0.1804	118.0366	-14.6213	60.1963

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and (resid 2 through 165 )
2	X-RAY DIFFRACTION	2	chain A and (resid 166 through 293 )
3	X-RAY DIFFRACTION	3	chain A and (resid 294 through 599 )
4	X-RAY DIFFRACTION	4	chain B and (resid 2 through 165 )
5	X-RAY DIFFRACTION	5	chain B and (resid 166 through 293 )
6	X-RAY DIFFRACTION	6	chain B and (resid 294 through 599 )
7	X-RAY DIFFRACTION	7	chain C and (resid 2 through 52 )
8	X-RAY DIFFRACTION	8	chain C and (resid 53 through 89 )
9	X-RAY DIFFRACTION	9	chain C and (resid 90 through 165 )
10	X-RAY DIFFRACTION	10	chain C and (resid 166 through 293 )
11	X-RAY DIFFRACTION	11	chain C and (resid 294 through 599 )

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