PDB-4qnl: Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C

ID or keywords:

Entry

Database: PDB / ID: 4qnl

Title

Crystal structure of tail fiber protein gp63.1 from E. coli phage G7C

Components

Tail fiber protein

Keywords

HYDROLASE / tail fiber / G7C phage / hydrolase-type esterase / SGNH hydrolase-type esterase domain (IPR013831) / Adsorption of the phage on bacterial host / bacterial LPS digestion / tail fiber protein gp66 / selenomethionine derivative / distal end of the baseplate

Function / homology

Function and homology information

Seminal Fluid Protein PDC-109 (Domain B) - #80 / NE0471 N-terminal domain-like - #50 / NE0471 N-terminal domain-like / Tail spike TSP1/Gp66, N-terminal domain / Tail spike TSP1/Gp66 receptor binding N-terminal domain /

Seminal Fluid Protein PDC-109 (Domain B) /

Ribbon / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology

Biological species

Escherichia phage vB_EcoP_G7C (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.411 Å

Authors

Riccio, C. / Browning, C. / Prokhorov, N. / Letarov, A. / Leiman, P.G.

Citation

Journal: Mol. Microbiol. / Year: 2017
Title: Function of bacteriophage G7C esterase tailspike in host cell adsorption.
Authors: Prokhorov, N.S. / Riccio, C. / Zdorovenko, E.L. / Shneider, M.M. / Browning, C. / Knirel, Y.A. / Leiman, P.G. / Letarov, A.V.

History

Deposition	Jun 18, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 4, 2015	Group: Structure summary
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Dec 20, 2017	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4qnl.cif.gz	337.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4qnl.ent.gz	286.7 KB	Display	PDB format
PDBx/mmJSON format	4qnl.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/qn/4qnl ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qnl	HTTPS FTP

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Related structure data

Similar structure data	2ifn-1 1ql1-1 1hh0-1 1ifp-1 1hgv-1 2xkm-1 4aq5-d 0227 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Tail fiber protein

hetero molecules

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

1

A: Tail fiber protein

hetero molecules

A: Tail fiber protein

hetero molecules

A: Tail fiber protein

hetero molecules

defined by author&software
287 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.773, 92.773, 551.926
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-906- ZN
2	1	A-1110- HOH
3	1	A-1185- HOH
4	1	A-1250- HOH
5	1	A-1264- HOH
6	1	A-1328- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Tail fiber protein Mass: 94838.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage vB_EcoP_G7C (virus) / Gene: 63.1, gp63.1 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: G0XNW5

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Non-polymers , 6 types, 341 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.41 Å³/Da / Density % sol: 48.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 150 mM Ammonium Sulphate, 34% PEE 797, 100 mM Bis-Tris pH 5.5; 1.5 ul protein @ 14.3 mg/ml + 1.5 ul well solution, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97969 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012 / Details: dynamically bendable mirror
Radiation	Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97969 Å / Relative weight: 1
Reflection	Resolution: 2.4→92 Å / Num. all: 67757 / Num. obs: 67757 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / B_iso Wilson estimate: 57.1 Å² / R_merge(I) obs: 0.075 / Net I/σ(I): 15.9
Reflection shell	Resolution: 2.41→2.56 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.72 / Mean I/σ(I) obs: 2 / Num. unique all: 10495 / % possible all: 94.4

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: dev_1647)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.411→64.959 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic with TLS / Cross valid method: FREE R / σ(F): 1.21 / Phase error: 23.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2207	1790	4.98 %	RANDOM
R_work	0.1594	-	-	-
obs	0.1624	67728	99.03 %	-
all	-	67757	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 51.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.411→64.959 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6509	0	39	330	6878

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6746
X-RAY DIFFRACTION	f_angle_d	0.801	9173
X-RAY DIFFRACTION	f_dihedral_angle_d	11.366	2413
X-RAY DIFFRACTION	f_chiral_restr	0.031	1000
X-RAY DIFFRACTION	f_plane_restr	0.003	1188

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 (%)
2.4114-2.4459	0.3136	113	0.2812	2214	X-RAY DIFFRACTION	79
2.4459-2.4824	0.3504	140	0.2415	2621	X-RAY DIFFRACTION	100
2.4824-2.5212	0.298	140	0.2262	2736	X-RAY DIFFRACTION	100
2.5212-2.5625	0.2962	138	0.2201	2721	X-RAY DIFFRACTION	100
2.5625-2.6067	0.2376	139	0.2129	2646	X-RAY DIFFRACTION	100
2.6067-2.6541	0.3135	143	0.2091	2742	X-RAY DIFFRACTION	100
2.6541-2.7051	0.2952	141	0.2099	2697	X-RAY DIFFRACTION	100
2.7051-2.7603	0.2837	141	0.1956	2682	X-RAY DIFFRACTION	100
2.7603-2.8204	0.2673	142	0.1976	2737	X-RAY DIFFRACTION	100
2.8204-2.886	0.3079	143	0.2017	2695	X-RAY DIFFRACTION	100
2.886-2.9581	0.2838	141	0.2025	2685	X-RAY DIFFRACTION	100
2.9581-3.0381	0.296	145	0.2078	2717	X-RAY DIFFRACTION	100
3.0381-3.1275	0.2351	140	0.2017	2709	X-RAY DIFFRACTION	100
3.1275-3.2285	0.2529	143	0.1841	2697	X-RAY DIFFRACTION	100
3.2285-3.3439	0.2598	145	0.1829	2706	X-RAY DIFFRACTION	100
3.3439-3.4777	0.2275	137	0.1637	2698	X-RAY DIFFRACTION	100
3.4777-3.636	0.2242	143	0.1628	2694	X-RAY DIFFRACTION	100
3.636-3.8277	0.1899	146	0.1317	2723	X-RAY DIFFRACTION	100
3.8277-4.0675	0.1987	141	0.1279	2699	X-RAY DIFFRACTION	100
4.0675-4.3814	0.1657	143	0.1123	2719	X-RAY DIFFRACTION	100
4.3814-4.8222	0.1653	145	0.1129	2681	X-RAY DIFFRACTION	100
4.8222-5.5197	0.1866	143	0.1242	2719	X-RAY DIFFRACTION	100
5.5197-6.953	0.1808	137	0.1514	2695	X-RAY DIFFRACTION	100
6.953-64.9826	0.2027	146	0.1517	2720	X-RAY DIFFRACTION	100

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	0.643	0.1327	-0.0769	0.4529	0.1777	0.5616	0.002	-0.085	0.0167	-0.022	0.0159	-0.1244	-0.1966	0.054	-0.0001	0.5846	-0.0066	0.0028	0.5418	-0.0235	0.5792	1.5346	13.2901	206.1886
2	0.7391	0.0972	0.1436	0.5763	-0.0361	0.9319	-0.0396	-0.035	-0.0619	-0.0181	0.0487	-0.1483	-0.0449	0.148	-0	0.3914	-0.0082	-0.0025	0.412	-0.0273	0.4174	23.628	7.9332	155.4441
3	0.2103	-0.0171	0.1249	0.0028	-0.0156	0.0922	0.1524	0.0409	-0.1946	0.098	0.0281	0.126	0.1747	-0.1164	0.0002	0.4792	0.0186	-0.0634	0.5182	-0.0189	0.5418	19.8351	-5.4725	154.1412
4	0.0655	0.041	0.0401	0.0581	0.0031	0.0394	0.0429	0.1544	-0.2245	-0.0918	0.1338	-0.1156	0.0866	-0.0293	0.0004	0.471	-0.0155	-0.0155	0.5314	-0.0335	0.4618	16.5879	-6.7044	143.0855
5	0.4931	-0.0581	0.0497	0.3702	-0.2618	0.8072	0.0442	0.0752	0.0092	-0.0316	0.0505	-0.0781	-0.0426	0.1098	-0	0.516	-0.0257	0.0584	0.4889	-0.0121	0.4426	14.0152	13.7361	121.7362
6	0.8531	0.1878	-0.5096	0.6644	-0.058	0.8155	0.0872	0.156	0.0192	-0.0526	0.0367	0.0234	-0.0167	-0.0538	-0.0001	0.5975	0.0257	0.0609	0.6023	0.0708	0.477	0.1932	17.9884	91.9583
7	0.0229	0.003	0.0011	0.0198	-0.0061	0.0026	-0.2892	-0.2122	-0.0285	-0.1398	0.1504	0.0965	0.0832	0.0937	0.0015	0.8899	-0.0959	0.0413	1.1404	-0.231	0.8591	20.4343	11.6152	82.5129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 13:162)
2	X-RAY DIFFRACTION	2	(chain A and resid 163:380)
3	X-RAY DIFFRACTION	3	(chain A and resid 381:405)
4	X-RAY DIFFRACTION	4	(chain A and resid 406:430)
5	X-RAY DIFFRACTION	5	(chain A and resid 431:679)
6	X-RAY DIFFRACTION	6	(chain A and resid 680:852)
7	X-RAY DIFFRACTION	7	(chain A and resid 853:859)

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