PDB-5aq5: Structure of the Carboxy-Terminal Domain of the Bacteriophage T5 ...

ID or keywords:

Entry

Database: PDB / ID: 5aq5

Title

Structure of the Carboxy-Terminal Domain of the Bacteriophage T5 L- Shaped Tail Fibre

Components

L-SHAPED TAIL FIBER PROTEIN PB8

Keywords

VIRAL PROTEIN

Function / homology

Function and homology information

lipopolysaccharide-mediated virion attachment to host cell / virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / symbiont entry into host cell / proteolysis
Similarity search - Function

Biological species

ESCHERICHIA PHAGE T5 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Garcia-Doval, C. / Granell, M. / van Raaij, M.J.

Citation

Journal: Viruses / Year: 2015
Title: Structure of the Receptor-Binding Carboxy-Terminal Domain of the Bacteriophage T5 L-Shaped Tail Fibre with and without Its Intra-Molecular Chaperone.
Authors: Garcia-Doval, C. / Caston, J.R. / Luque, D. / Granell, M. / Otero, J.M. / Llamas-Saiz, A.L. / Renouard, M. / Boulanger, P. / van Raaij, M.J.

History

Deposition	Sep 19, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 30, 2015	Group: Database references
Revision 1.2	Jan 17, 2018	Group: Database references / Category: citation / citation_author Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5aq5.cif.gz	1.2 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	5aq5_validation.pdf.gz	560.8 KB	Display	wwPDB validaton report
Full document	5aq5_full_validation.pdf.gz	603.4 KB	Display
Data in XML	5aq5_validation.xml.gz	115.2 KB	Display
Data in CIF	5aq5_validation.cif.gz	159.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aq/5aq5 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/5aq5	HTTPS FTP

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Related structure data

Related structure data	4uw7SC 4uw8C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3gr9-2 1anj-d 1kh9-d 1kh4-d 1ali-d 1khn-d 1aja-d 1ani-d 1alh-d 1hqa-d 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

Related structure data

4uw7SC

4uw8C

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-SHAPED TAIL FIBER PROTEIN PB8

B: L-SHAPED TAIL FIBER PROTEIN PB8

C: L-SHAPED TAIL FIBER PROTEIN PB8

D: L-SHAPED TAIL FIBER PROTEIN PB8

E: L-SHAPED TAIL FIBER PROTEIN PB8

F: L-SHAPED TAIL FIBER PROTEIN PB8

G: L-SHAPED TAIL FIBER PROTEIN PB8

H: L-SHAPED TAIL FIBER PROTEIN PB8

I: L-SHAPED TAIL FIBER PROTEIN PB8

J: L-SHAPED TAIL FIBER PROTEIN PB8

K: L-SHAPED TAIL FIBER PROTEIN PB8

L: L-SHAPED TAIL FIBER PROTEIN PB8

413 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-SHAPED TAIL FIBER PROTEIN PB8

B: L-SHAPED TAIL FIBER PROTEIN PB8

C: L-SHAPED TAIL FIBER PROTEIN PB8

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

2

D: L-SHAPED TAIL FIBER PROTEIN PB8

E: L-SHAPED TAIL FIBER PROTEIN PB8

F: L-SHAPED TAIL FIBER PROTEIN PB8

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

3

G: L-SHAPED TAIL FIBER PROTEIN PB8

H: L-SHAPED TAIL FIBER PROTEIN PB8

I: L-SHAPED TAIL FIBER PROTEIN PB8

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

4

J: L-SHAPED TAIL FIBER PROTEIN PB8

K: L-SHAPED TAIL FIBER PROTEIN PB8

L: L-SHAPED TAIL FIBER PROTEIN PB8

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

Unit cell

Length a, b, c (Å)	86.623, 95.029, 127.748
Angle α, β, γ (deg.)	68.24, 70.20, 83.63
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J
11	1	K
12	1	L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 1 / Auth seq-ID: 990 - 1263 / Label seq-ID: 55 - 328

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J
11	K	K
12	L	L

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.496966, -0.75477, 0.428192), (0.792203, -0.193216, 0.578863), (-0.354175, 0.62689, 0.693952)	79.62507, 22.27469, -13.71885
3	given	(-0.50095, 0.79051, -0.35234), (-0.752372, -0.196548, 0.628732), (0.427767, 0.580054, 0.693219)	17.23924, 73.08784, -37.45229
4	given	(-0.515924, 0.754467, -0.40571), (0.783516, 0.224147, -0.579536), (-0.346302, -0.616877, -0.70678)	29.91119, -64.23843, -12.73404
5	given	(-0.481175, -0.809776, 0.335757), (-0.760758, 0.195428, -0.618915), (0.435566, -0.553236, -0.710079)	107.58967, 51.08952, -73.61925
6	given	(0.99972, 0.022655, -0.006765), (0.022473, -0.999413, -0.025849), (-0.007347, 0.02569, -0.999643)	-44.21111, 54.68492, -70.72798
7	given	(0.264553, 0.856436, -0.443316), (-0.344454, 0.513288, 0.786058), (0.900757, -0.055252, 0.430795)	-63.79435, 69.57909, -14.20215
8	given	(0.515472, -0.836327, -0.186671), (0.797019, 0.547941, -0.25401), (0.31472, -0.017845, 0.949017)	52.79275, -50.04299, 42.5342
9	given	(-0.722022, -0.006416, 0.69184), (0.437835, -0.778496, 0.449716), (0.535709, 0.627617, 0.5649)	109.39558, 98.2277, -34.32628
10	given	(0.499287, -0.839589, -0.214015), (-0.799878, -0.54159, 0.258602), (-0.333028, 0.04207, -0.941978)	52.78648, 151.9415, -1.77669
11	given	(0.210711, 0.84389, -0.493407), (0.356992, -0.536306, -0.764809), (-0.910032, -0.014989, -0.414267)	-61.90518, 33.70916, 61.78873
12	given	(-0.76378, -0.023904, 0.645034), (-0.430212, 0.763844, -0.481104), (-0.481205, -0.644958, -0.593692)	111.59644, 2.61394, 72.05231

#1: Protein	L-SHAPED TAIL FIBER PROTEIN PB8 / LTF / L-SHAPED TAIL FIBRES Mass: 34457.211 Da / Num. of mol.: 12 / Fragment: C-TERMINAL DOMAIN, UNP 970-1263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA PHAGE T5 (virus) / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q66LT2, UniProt: P13390*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

L-SHAPED TAIL FIBER PROTEIN PB8 / LTF / L-SHAPED TAIL FIBRES

Mass: 34457.211 Da / Num. of mol.: 12 / Fragment: C-TERMINAL DOMAIN, UNP 970-1263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA PHAGE T5 (virus) / Plasmid: PET-28A / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q66LT2, UniProt: P13390*PLUS

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.22 Å³/Da / Density % sol: 44.8 % / Description: NONE
Crystal grow	pH: 8.5 Details: 0.1 M TRIS-HCL PH 8.5, 8% (W/V) PEG 4000, 10 MM IRON(III) CHLORIDE, 20% (V/V) GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014 Details: VERTICAL FOCUSING MIRROR AND HORIZONTAL FOCUSING MIRROR ORTHOGONAL IN A KIRKPATRICK-BAEZ CONFIGURATION
Radiation	Monochromator: CRYOGENICALLY COOLED CHANNEL-CUT DCM SI (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.3→23 Å / Num. obs: 144381 / % possible obs: 91.3 % / Redundancy: 2.4 % / R_merge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 2.4 % / R_merge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / % possible all: 90.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UW7

4uw7

Resolution: 2.3→23 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.918 / SU B: 25.654 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25228	2906	2 %	THIN SHELLS
R_work	0.22297	-	-	-
obs	0.22354	140892	90.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 62.601 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.66 Å²	2.03 Å²	-2.16 Å²
2-	-	2.54 Å²	-1.05 Å²
3-	-	-	-2.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24486	0	0	858	25344

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	25074
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.326	1.938	34128
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.128	5	3290
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.56	23.037	1034
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.454	15	3688
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.48	15	192
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	3698
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	19516
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.167	0.2	21792
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.289	0.2	33096
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.087	0.2	1764
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.354	0.2	76
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.303	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.596	2.365	13196
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.044	3.545	16474
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.62	2.401	11878
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.038	3.579	17654
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 2033 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-ID	Auth asym-ID	Rms dev position (Å)
1	A	5.05
2	B	4.8
3	C	4.29
4	D	3.58
5	E	3.59
6	F	4.48
7	G	4.19
8	H	5.29
9	I	5.24
10	J	4.78
11	K	4.74
12	L	4.14

LS refinement shell

Resolution: 2.3→2.423 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.306	467	-
R_work	0.29	20160	-
obs	-	-	89.87 %

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	0.8465	0.0077	0.0705	1.0254	0.817	2.2297	0.0345	-0.0874	0.1195	0.0324	0.0842	-0.1414	-0.3051	0.0874	-0.1187	0.3038	0.0178	0.0782	0.2608	-0.1118	0.0985	32.9067	40.2135	-15.9634
2	0.8109	-0.0203	0.0935	0.8571	0.8429	2.9096	0.0259	-0.1318	0.0247	0.2207	0.1552	-0.2005	0.1265	0.2601	-0.1811	0.2721	0.0345	0.0317	0.2875	-0.1427	0.1291	38.1417	30.5138	-11.0582
3	0.8983	-0.0245	-0.0766	0.9952	1.0243	2.8507	-0.0082	-0.1439	0.0068	0.1921	0.0418	-0.0256	0.0635	-0.1196	-0.0336	0.2361	0.0276	0.0594	0.2702	-0.0988	0.0654	26.1959	31.448	-11.1844
4	0.9485	0.0731	0.5019	0.8239	0.7218	2.6625	-0.0349	0.1623	-0.0071	-0.2202	0.1066	-0.1239	-0.1699	0.4154	-0.0716	0.2595	-0.0134	0.1029	0.2254	-0.0686	0.0692	81.4022	27.6448	-59.4706
5	0.975	0.0061	0.6089	0.7335	0.7718	2.5873	-0.0228	0.1119	-0.0188	-0.1661	-0.0065	-0.0102	-0.1837	-0.0153	0.0293	0.2572	0.0266	0.0735	0.15	-0.0508	0.0485	69.3297	26.4409	-59.2961
6	1.2305	-0.1725	0.2949	1.1866	1.0627	2.3525	0.1083	0.086	-0.196	-0.0194	0.0981	-0.1063	0.2212	0.182	-0.2063	0.2554	0.0343	0.047	0.1184	-0.0537	0.0799	76.3759	17.613	-54.9051
7	1.1488	0.0123	0.9552	1.1302	0.1646	2.1834	-0.1869	-0.2572	0.1821	-0.1065	-0.0761	0.3203	-0.4032	-0.5208	0.263	0.6342	0.1712	-0.1174	0.4368	-0.1315	0.4003	34.1584	67.8411	-66.7264
8	1.9014	-0.1176	1.4507	1.0283	0.0155	2.3294	-0.1723	0.101	0.2048	-0.2068	-0.0304	0.1692	-0.3755	-0.0741	0.2026	0.6361	0.0825	-0.0826	0.3077	-0.0679	0.278	43.3123	67.1387	-74.7314
9	1.745	-0.1288	1.6136	0.9486	-0.0635	2.9825	0.0001	-0.079	-0.0622	-0.1458	-0.0052	0.2172	-0.0827	-0.3334	0.0051	0.5102	0.0926	-0.0475	0.2679	-0.0718	0.3	39.6743	57.1917	-68.6463
10	1.4731	0.5455	1.6001	1.3137	0.9305	2.6217	-0.1452	-0.2149	0.102	0.0235	0.0873	0.0457	-0.1754	-0.322	0.0579	0.6736	0.1132	-0.034	0.451	-0.0934	0.2994	84.1204	76.6157	-11.2672
11	1.3697	0.343	1.3564	0.9571	0.6265	2.6504	-0.2029	0.1393	0.103	-0.1243	0.2336	-0.0766	-0.3369	0.2283	-0.0307	0.7129	0.0189	-0.0321	0.4409	-0.1255	0.3485	93.0009	77.6712	-19.5246
12	1.3921	0.1823	1.2188	0.9372	0.4542	2.1726	-0.4121	-0.0096	0.3501	-0.2026	0.1637	0.044	-0.6235	-0.0362	0.2484	0.8798	0.0605	-0.133	0.4696	-0.1289	0.4668	86.2516	87.3437	-16.6018

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	989 - 1263
2	X-RAY DIFFRACTION	2	B	988 - 1263
3	X-RAY DIFFRACTION	3	C	988 - 1263
4	X-RAY DIFFRACTION	4	D	989 - 1263
5	X-RAY DIFFRACTION	5	E	989 - 1263
6	X-RAY DIFFRACTION	6	F	989 - 1263
7	X-RAY DIFFRACTION	7	G	989 - 1263
8	X-RAY DIFFRACTION	8	H	989 - 1263
9	X-RAY DIFFRACTION	9	I	989 - 1263
10	X-RAY DIFFRACTION	10	J	989 - 1263
11	X-RAY DIFFRACTION	11	K	989 - 1263
12	X-RAY DIFFRACTION	12	L	989 - 1263

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About Yorodumi

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Yorodumi