PDB-4jpn: Bacteriophage phiX174 H protein residues 143-221

ID or keywords:

Entry

Database: PDB / ID: 4jpn

Title

Bacteriophage phiX174 H protein residues 143-221

Components

Minor spike protein H

Keywords

VIRAL PROTEIN / helical barrel / tail tube / pilot DNA during phage infection

Function / homology

Function and homology information

lipopolysaccharide-mediated virion attachment to host cell / viral capsid / symbiont entry into host cell / identical protein binding
Similarity search - Function

Biological species

Enterobacteria phage phiX174 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.101 Å

Authors

Sun, L. / Young, L.N. / Boudko, S.B. / Fokine, A. / Zhang, X. / Rossmann, M.G. / Fane, B.A.

Citation

Journal: Nature / Year: 2014
Title: Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection.
Authors: Lei Sun / Lindsey N Young / Xinzheng Zhang / Sergei P Boudko / Andrei Fokine / Erica Zbornik / Aaron P Roznowski / Ian J Molineux / Michael G Rossmann / Bentley A Fane /

Abstract: Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on ...

History

Deposition	Mar 19, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 15, 2014	Group: Database references
Revision 1.2	Jan 22, 2014	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4jpn.cif.gz	318.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4jpn.ent.gz	264.6 KB	Display	PDB format
PDBx/mmJSON format	4jpn.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/jp/4jpn ftp://data.pdbj.org/pub/pdb/validation_reports/jp/4jpn	HTTPS FTP

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Related structure data

Related structure data	4jppC C: citing same article (ref.)
Similar structure data	2olt-1 2olt-3 2iiu-2 1qxe-2 6c4r-1 3tj7-d 3p1u-d 1qxd-2 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: Minor spike protein H

B: Minor spike protein H

C: Minor spike protein H

D: Minor spike protein H

E: Minor spike protein H

F: Minor spike protein H

G: Minor spike protein H

H: Minor spike protein H

I: Minor spike protein H

J: Minor spike protein H

90.1 kDa, 10 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)	83.372, 193.904, 67.379
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-341- HOH

#1: Protein	Minor spike protein H / H protein / Pilot protein Mass: 9008.977 Da / Num. of mol.: 10 / Fragment: coiled coil domain (UNP residues 143-221) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Gene: H / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03646
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Minor spike protein H / H protein / Pilot protein

Mass: 9008.977 Da / Num. of mol.: 10 / Fragment: coiled coil domain (UNP residues 143-221)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Enterobacteria phage phiX174 (virus) / Gene: H / Plasmid: pET22b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03646

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG1000, 0.2 M magnesium chloride, 0.6% n-Octyl-beta-D-glucoside, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-B	1	1.5418
SYNCHROTRON	APS	23-ID-B	2	0.97944

Detector

Type	ID	Detector	Date
MARMOSAIC 300 mm CCD	1	CCD	Mar 24, 2012
MARMOSAIC 300 mm CCD	2	CCD	Mar 24, 2012

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Double crystal cryo-cooled Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Double crystal cryo-cooled Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97944	1

Reflection

Resolution: 2.1→20 Å / Num. all: 64298 / Num. obs: 64298 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.3 % / R_merge(I) obs: 0.086 / Net I/σ(I): 32.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Diffraction-ID	% possible all
2.1-2.17	11.2	0.269	6333	1,2	100
2.17-2.26	11.2	0.221	6364	1,2	100
2.26-2.36	11.3	0.184	6349	1,2	100
2.36-2.49	11.3	0.155	6410	1,2	100
2.49-2.64	11.3	0.132	6356	1,2	100
2.64-2.85	11.4	0.105	6423	1,2	100
2.85-3.13	11.4	0.083	6422	1,2	100
3.13-3.59	11.4	0.088	6488	1,2	100
3.59-4.51	11.4	0.066	6511	1,2	99.6
4.51-20	11.2	0.054	6642	1,2	97.9

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Processing

Software

Name	Version	Classification
Locally	modified Blu-Ice GUI interface to EPICS control	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.101→19.912 Å / SU ML: 0.18 / σ(F): 1.38 / Phase error: 20.81 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2164	3248	5.06 %	RANDOM
R_work	0.1732	-	-	-
all	0.176	64298	-	-
obs	0.1755	64225	99.6 %	-

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.101→19.912 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5912	0	0	935	6847

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5932
X-RAY DIFFRACTION	f_angle_d	0.874	7936
X-RAY DIFFRACTION	f_dihedral_angle_d	16.073	2346
X-RAY DIFFRACTION	f_chiral_restr	0.058	881
X-RAY DIFFRACTION	f_plane_restr	0.003	1083

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 (%)
2.101-2.132	0.2256	152	0.1589	2519	X-RAY DIFFRACTION	97
2.132-2.1653	0.2092	157	0.1621	2608	X-RAY DIFFRACTION	100
2.1653-2.2008	0.2088	135	0.1557	2638	X-RAY DIFFRACTION	100
2.2008-2.2387	0.2269	149	0.1583	2627	X-RAY DIFFRACTION	100
2.2387-2.2793	0.2332	138	0.1649	2624	X-RAY DIFFRACTION	100
2.2793-2.3231	0.2293	142	0.1684	2639	X-RAY DIFFRACTION	100
2.3231-2.3704	0.2402	153	0.1677	2591	X-RAY DIFFRACTION	100
2.3704-2.4219	0.2193	135	0.1687	2625	X-RAY DIFFRACTION	100
2.4219-2.4781	0.2397	129	0.1717	2667	X-RAY DIFFRACTION	100
2.4781-2.54	0.2382	125	0.1685	2658	X-RAY DIFFRACTION	100
2.54-2.6085	0.2229	148	0.1679	2661	X-RAY DIFFRACTION	100
2.6085-2.6851	0.2253	139	0.1647	2631	X-RAY DIFFRACTION	100
2.6851-2.7715	0.2119	132	0.1736	2637	X-RAY DIFFRACTION	100
2.7715-2.8703	0.2313	151	0.1871	2636	X-RAY DIFFRACTION	100
2.8703-2.9849	0.242	163	0.1759	2650	X-RAY DIFFRACTION	100
2.9849-3.1202	0.2363	125	0.1851	2661	X-RAY DIFFRACTION	100
3.1202-3.2841	0.1992	146	0.1851	2646	X-RAY DIFFRACTION	100
3.2841-3.4888	0.1974	139	0.1668	2684	X-RAY DIFFRACTION	100
3.4888-3.7565	0.172	156	0.1449	2681	X-RAY DIFFRACTION	100
3.7565-4.1315	0.2069	137	0.1602	2693	X-RAY DIFFRACTION	100
4.1315-4.7223	0.2033	126	0.1656	2713	X-RAY DIFFRACTION	99
4.7223-5.9236	0.2428	126	0.226	2727	X-RAY DIFFRACTION	99
5.9236-19.9129	0.2257	145	0.1967	2761	X-RAY DIFFRACTION	96

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	0.3482	-0.1246	0.2456	2.2409	-1.5098	1.8554	0.048	-0.0704	0.019	0.0784	0.0144	0.0753	-0.0401	-0.1436	-0.0432	0.0828	-0.0071	-0.0151	0.2212	-0.0001	0.1583	-34.3235	20.2645	-2.6299
2	0.337	0.0719	-0.0705	1.4675	-0.1122	0.521	0.0945	-0.0617	-0.0288	0.0648	-0.0176	0.139	0.0313	-0.1468	-0.0347	0.1003	-0.0501	-0.0403	0.2282	0.0068	0.1808	-36.6699	12.7801	-9.2185
3	0.4071	-0.295	0.1623	0.9222	0.5596	0.6283	0.008	-0.0327	-0.0669	-0.0091	0.0551	0.0689	0.0349	-0.1895	-0.0487	0.0977	-0.0483	-0.044	0.1892	0.0058	0.1806	-32.314	7.847	-18.7248
4	0.7161	0.2457	-0.157	3.1484	-1.9049	3.2396	0.0493	-0.0666	-0.2061	-0.1655	-0.0714	-0.0302	0.0917	0.1177	0.0518	0.1204	-0.0083	0.0001	0.2012	-0.0104	0.2025	-23.9362	3.6441	-21.6939
5	0.8317	0.1937	0.1027	1.8589	-0.4376	1.3132	-0.0075	0.0399	-0.1527	-0.1686	0.0574	-0.1738	0.0755	0.0545	0.0435	0.1411	-0.0058	0.0607	0.1949	-0.0364	0.2348	-13.6677	4.2959	-20.6404
6	0.4625	0.625	-0.125	3.7178	-2.0603	2.3806	0.0208	0.0084	-0.096	-0.2786	0.0102	-0.1794	0.2854	0.1609	0.0417	0.0774	0.0262	0.0947	0.2658	-0.0015	0.3221	-6.6207	6.6521	-14.131
7	0.3644	0.445	-0.4566	6.2582	-4.5361	3.8242	-0.059	-0.0231	-0.1161	0.2271	-0.0255	-0.307	-0.1709	0.1263	0.069	0.1047	-0.0183	0.0058	0.2789	0.0282	0.3182	-3.892	14.3723	-6.9691
8	0.4943	0.1929	-0.4342	3.2963	-2.4026	2.923	-0.0244	-0.0579	-0.0707	0.1506	0.0458	-0.0699	-0.13	0.1695	-0.0241	0.1002	-0.0302	-0.0173	0.2527	0.0412	0.2667	-7.5054	21.5672	-0.6599
9	0.2833	0.5174	-0.5045	5.2615	-4.2978	4.7826	-0.0029	-0.0872	-0.0235	0.045	0.1323	0.1028	-0.0362	-0.0272	-0.093	0.0803	0.0051	-0.0203	0.1957	0.0166	0.2244	-16.3242	26.0888	2.4483
10	0.4149	0.4559	-0.2453	6.4969	-5.9262	6.6803	0.1052	-0.0884	-0.0025	0.1853	-0.097	-0.0003	-0.1246	0.0192	0.0231	0.0888	0.0117	-0.0111	0.1909	-0.023	0.1897	-26.0941	24.5847	3.0764

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resseq 144:218)
2	X-RAY DIFFRACTION	2	(chain B and resseq 144:217)
3	X-RAY DIFFRACTION	3	(chain C and resseq 145:221)
4	X-RAY DIFFRACTION	4	(chain D and resseq 145:220)
5	X-RAY DIFFRACTION	5	(chain E and resseq 145:220)
6	X-RAY DIFFRACTION	6	(chain F and resseq 145:216)
7	X-RAY DIFFRACTION	7	(chain G and resseq 144:218)
8	X-RAY DIFFRACTION	8	(chain H and resseq 145:218)
9	X-RAY DIFFRACTION	9	(chain I and resseq 145:219)
10	X-RAY DIFFRACTION	10	(chain J and resseq 145:216)

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