PDB-3u6x: Phage TP901-1 baseplate tripod

ID or keywords:

Entry

Database: PDB / ID: 3u6x

Title

Phage TP901-1 baseplate tripod

Components

BPP
ORF48

Keywords

VIRAL PROTEIN / helix/beta / receptor binding complex / phage tail baseplate

Function / homology

Function and homology information

virus tail, baseplate / cell adhesion / virion attachment to host cell
Similarity search - Function

Biological species

Lactococcus phage TP901-1 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Veesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V.I. / van Sinderen, D. / Cambillau, C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the phage TP901-1 1.8 MDa baseplate suggests an alternative host adhesion mechanism.
Authors: Veesler, D. / Spinelli, S. / Mahony, J. / Lichiere, J. / Blangy, S. / Bricogne, G. / Legrand, P. / Ortiz-Lombardia, M. / Campanacci, V. / van Sinderen, D. / Cambillau, C.

History

Deposition	Oct 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 4, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 11, 2012	Group: Database references
Revision 1.2	Sep 13, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3u6x.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb3u6x.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	3u6x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3u6x_validation.pdf.gz	586.7 KB	Display	wwPDB validaton report
Full document	3u6x_full_validation.pdf.gz	621.8 KB	Display
Data in XML	3u6x_validation.xml.gz	160.8 KB	Display
Data in CIF	3u6x_validation.cif.gz	228.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u6/3u6x ftp://data.pdbj.org/pub/pdb/validation_reports/u6/3u6x	HTTPS FTP

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Related structure data

Related structure data	3uh8C 4v96C 3ejcS 2f0c S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3hi8-d 3wi6-d 3e1j-d 1ykm-d 3lkt-d 3mi5-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) 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
Related items in Molecule of the Month	#132 - Dec 2010 Adenovirus similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: BPP

B: BPP

C: BPP

D: BPP

E: BPP

F: BPP

G: BPP

H: BPP

I: BPP

J: BPP

K: BPP

L: BPP

M: BPP

N: BPP

O: BPP

P: BPP

Q: BPP

R: BPP

S: ORF48

T: ORF48

U: ORF48

X: ORF48

Y: ORF48

Z: ORF48

hetero molecules

383 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BPP

B: BPP

C: BPP

D: BPP

E: BPP

F: BPP

G: BPP

H: BPP

I: BPP

X: ORF48

Y: ORF48

Z: ORF48

hetero molecules

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

2

J: BPP

K: BPP

L: BPP

M: BPP

N: BPP

O: BPP

P: BPP

Q: BPP

R: BPP

S: ORF48

T: ORF48

U: ORF48

hetero molecules

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

Unit cell

Length a, b, c (Å)	149.960, 237.420, 152.210
Angle α, β, γ (deg.)	90.00, 115.67, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	BPP / Baseplate protein Mass: 17303.387 Da / Num. of mol.: 18 / Fragment: ORF49 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, ORF49 / Plasmid: pET22AGW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys / References: UniProt: Q9G096
#2: Protein	ORF48 Mass: 11610.187 Da / Num. of mol.: 6 / Fragment: ORF48 195-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: ORF48 / Plasmid: pET22AGW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLys / References: UniProt: Q9AZ56
#3: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Br
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3492 / 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: 6.41 Å³/Da / Density % sol: 80.8 %
Crystal grow	Temperature: 273 K / pH: 7.2 Details: Concentration of tripod: 5.3 mg/ml, 25% PEG1000, 0.1 M HEPES pH 7.2, , VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9791
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2011 / Details: MIRRORS
Radiation	Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 2.6→50 Å / Num. obs: 298571 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / B_iso Wilson estimate: 53.18 Å² / R_merge(I) obs: 0.079 / R_sym value: 0.079 / Net I/σ(I): 10.3
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 2.55 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / R_sym value: 0.48 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
BUSTER	2.9.2	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EJC

3ejc

Resolution: 2.6→49.74 Å / Cor.coef. F_o:F_c: 0.8801 / Cor.coef. F_o:F_c free: 0.8602 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2064	28781	9.98 %	RANDOM
R_work	0.1784	-	-	-
obs	0.1812	288313	-	-
all	-	288313	-	-

Displacement parameters

B_iso mean: 49.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-24.157 Å²	0 Å²	-1.1568 Å²
2-	-	25.9395 Å²	0 Å²
3-	-	-	-1.7825 Å²

Refine analyze

Luzzati coordinate error obs: 0.315 Å

Refinement step

Cycle: LAST / Resolution: 2.6→49.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26570	0	18	3492	30080

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	27086	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.23	36685	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		9177	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		599	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		3990	HARMONIC	5
X-RAY DIFFRACTION	t_it		27086	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		1	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	3.18
X-RAY DIFFRACTION	t_other_torsion	19.52
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion	0	3648	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	0	30299	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.6→2.67 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2709	2172	10.17 %
R_work	0.23	19190	-
all	0.2341	21362	-

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	0.2163	0.1519	-0.2169	0.1627	0.1923	-0.0336	-0.0125	0.017	0.0089	0.0088	-0.0012	-0.0052	0.0081	-0.0039	0.0137	-0.0093	0.0057	0.0214	-0.0194	0.0245	0.0108	-92.4296	-3.821	67.3598
2	0.2976	0.5006	-0.2658	0.2349	-0.1885	-0.1819	-0.0111	0.016	0.0178	-0.0014	0.0043	0.0029	0.0111	-0.0151	0.0068	-0.0195	0.0008	0.0289	-0.0233	0.0277	0.0195	-105.5344	-3.3664	58.918
3	0.1392	0.0585	-0.1382	0.1976	0.261	-0.0272	0.001	0.017	0.0064	0.0006	0.0081	0.0003	0.0079	0.0052	-0.0092	-0.0204	-0.0238	0.0386	-0.0197	0.0092	0.0168	-91.7663	-4.8224	51.8855
4	-0.0344	0.1156	0.0105	0.282	-0.1511	0.1053	-0.0185	-0.0116	-0.0123	0.009	-0.0089	-0.0043	0.0124	0.015	0.0275	0.0394	0.0163	-0.0237	-0.0082	-0.0252	-0.0404	-64.9232	-5.9908	28.6452
5	-0.078	0.2193	0.0433	0.1767	0.0579	0.1576	-0.0034	0.0141	-0.0056	0.0016	-0.0032	0.0026	0.006	0.0124	0.0066	0.0239	-0.0135	0	-0.0094	-0.0023	-0.0318	-77.8013	-3.2779	20.4052
6	-0.042	0.0415	0.0784	0.2689	0.5454	0.1879	-0.0079	0.0005	0.0031	0.0044	0.0021	-0.0052	0.0084	0.0116	0.0058	0.024	-0.0076	-0.0051	-0.0081	-0.016	-0.0333	-64.0264	-4.8805	13.1751
7	0.236	-0.5047	0.3074	0.1359	0.5166	0.241	-0.0195	-0.0141	-0.0004	0.0006	-0.0031	-0.0026	0.0206	0.0128	0.0226	-0.0154	0.013	-0.0334	-0.0011	-0.0151	-0.0024	-45.1048	-7.5844	72.0377
8	0.024	0.1308	0.1101	0.1853	0.5615	0.1002	-0.0223	0.0064	0.0141	-0.0021	0.0066	0.0009	0.0257	-0.0151	0.0156	-0.0232	0.0255	-0.0232	-0.0103	0.0232	0.0227	-58.0972	-7.3986	63.5252
9	0.1541	0.3885	0.1082	0.0054	-0.1155	0.0684	-0.0136	0.0158	0.0029	-0.0009	0.0007	-0.004	0.0169	0.0077	0.0129	-0.0145	0.0054	-0.0303	-0.0037	-0.0053	0.0019	-44.2653	-6.3437	56.4953
10	-0.0744	-0.0574	0.0381	0.2209	-0.6287	0.2354	-0.0024	-0.0147	0.0022	-0.0006	0.0045	0.0018	0.0075	-0.0084	-0.0021	0.033	-0.0171	-0.0066	-0.0083	0.036	-0.031	-80.9616	68.933	7.7982
11	-0.1009	-0.0613	0.0808	0.3881	0.187	0.1009	-0.0263	-0.0176	0.0146	0.0019	-0.0013	0.0092	0.0132	-0.0097	0.0275	0.0299	0.0111	0.0052	-0.0127	0.0451	-0.0299	-77.9413	70.4908	22.9356
12	-0.1435	-0.0682	0.1313	0.2317	-0.0555	0.1921	-0.0054	0.0067	0.0019	-0.0048	-0.0014	-0.0068	-0.0016	-0.0181	0.0067	0.0164	-0.0174	0.0061	-0.009	-0.0117	-0.0029	-66.1871	69.4966	12.8289
13	0.2937	-0.5759	-0.1891	0.2931	0.1972	-0.102	-0.0104	-0.0035	0.0052	0.0057	0.0029	-0.0029	0.0176	0.0024	0.0074	0.0029	0.0042	0.0309	-0.0269	-0.0021	0.0012	-91.1054	70.567	68.7385
14	0.0738	0.0969	-0.0738	0.4119	-0.3461	-0.0124	0.0004	-0.009	-0.0065	0.0024	-0.0026	-0.0051	-0.0011	0.0086	0.0022	-0.0078	0.0046	0.0307	-0.0171	-0.0251	0.0257	-79.4998	71.5342	58.4711
15	0.1938	-0.0961	-0.1918	0.3105	-0.2469	-0.0408	-0.0052	-0.0221	0.0031	-0.0008	-0.0012	0.0011	0.0064	0.0129	0.0064	-0.0044	0.0203	0.0393	-0.0212	0.0152	0.0028	-93.9621	68.9688	53.4862
16	0.2933	-0.3298	0.0497	0.1458	1.5415	-0.0199	-0.0229	-0.0002	-0.0219	-0.0062	-0.0064	-0.0038	0.0421	0.0166	0.0293	-0.0356	0.001	-0.0105	-0.0055	-0.0157	0.0182	-33.1356	73.5203	46.9863
17	0.1713	-0.4514	0.0806	0.2104	0.3623	0.0379	-0.0139	0.0075	-0.0138	-0.0034	-0.0012	-0.0059	0.0287	0.0022	0.0151	-0.006	-0.0288	-0.0166	-0.0062	-0.0194	0.008	-47.8597	73.1314	42.0237
18	0.0299	0.2759	0.1368	0.0818	-0.7787	0.1246	-0.0101	-0.0051	-0.0166	0.0038	0.0001	-0.0011	0.0276	0.0132	0.01	-0.0179	-0.0007	-0.0215	-0.0091	0.0035	0.0089	-44.8784	72.2436	57.2063
19	0.6238	0.107	0.164	0	0.1767	0.3523	0.0005	0	0.0019	-0.0038	0.0004	0.0092	0.0001	0.0005	-0.0009	0.005	-0.0008	-0.0054	0.0253	-0.0083	-0.0121	-83.9946	132.589	26.4571
20	0.8119	0.1014	-0.2979	0.2223	-0.2319	0.2927	0.0018	0.0003	-0.0004	0.0001	-0.0017	-0.0073	-0.0023	0.0005	0	-0.0036	-0.0091	-0.0204	0.0348	-0.0077	-0.0145	-56.1581	134.522	35.4227
21	0.1489	0.1404	0.062	0.1834	0.4465	0.4735	0.0004	0	0.0012	0.0098	-0.0004	0.0078	-0.0034	0.0061	0	-0.0042	-0.0143	0.0101	0.0194	-0.0065	0.0022	-77.9161	133.846	55.0896
22	0.1658	0.024	-0.113	0.1845	-0.0603	-0.0007	0.0004	-0.0014	-0.0002	0.0074	0.0018	-0.0055	0.0016	-0.0033	-0.0021	0.0142	0.0112	0.003	-0.0027	0.002	-0.0018	-67.8561	-68.8093	61.3879
23	-0.034	-0.1918	0.0322	0.2733	0.0435	0.1799	0.0001	0.0003	-0.001	-0.0034	-0.0002	-0.0047	-0.0009	0.0012	0.0002	0.015	-0.0009	0.0102	-0.0009	-0.0082	-0.0012	-66.3036	-68.0274	32.0873
24	0.1255	-0.0422	-0.1505	0.626	0.1755	0.0832	-0.0001	0.0071	-0.0008	0.0028	-0.0013	0.0069	0.0017	0.0002	0.0014	-0.0016	-0.0028	0.0307	-0.0049	-0.0051	0.0103	-92.424	-66.8819	45.434

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|2 - 163}	A	2 - 163
2	X-RAY DIFFRACTION	2	{B\|2 - 163}	B	2 - 163
3	X-RAY DIFFRACTION	3	{C\|2 - 163}	C	2 - 163
4	X-RAY DIFFRACTION	4	{D\|2 - 163}	D	2 - 163
5	X-RAY DIFFRACTION	5	{E\|2 - 163}	E	2 - 163
6	X-RAY DIFFRACTION	6	{F\|2 - 163}	F	2 - 163
7	X-RAY DIFFRACTION	7	{G\|2 - 163}	G	2 - 163
8	X-RAY DIFFRACTION	8	{H\|2 - 163}	H	2 - 163
9	X-RAY DIFFRACTION	9	{I\|2 - 163}	I	2 - 163
10	X-RAY DIFFRACTION	10	{J\|2 - 163}	J	2 - 163
11	X-RAY DIFFRACTION	11	{K\|2 - 163}	K	2 - 163
12	X-RAY DIFFRACTION	12	{L\|2 - 163}	L	2 - 163
13	X-RAY DIFFRACTION	13	{M\|2 - 163}	M	2 - 163
14	X-RAY DIFFRACTION	14	{N\|2 - 163}	N	2 - 163
15	X-RAY DIFFRACTION	15	{O\|2 - 163}	O	2 - 163
16	X-RAY DIFFRACTION	16	{P\|2 - 163}	P	2 - 163
17	X-RAY DIFFRACTION	17	{Q\|2 - 163}	Q	2 - 163
18	X-RAY DIFFRACTION	18	{R\|2 - 163}	R	2 - 163
19	X-RAY DIFFRACTION	19	{S\|195 - 299}	S	195 - 299
20	X-RAY DIFFRACTION	20	{T\|195 - 299}	T	195 - 299
21	X-RAY DIFFRACTION	21	{U\|195 - 299}	U	195 - 299
22	X-RAY DIFFRACTION	22	{X\|195 - 299}	X	195 - 299
23	X-RAY DIFFRACTION	23	{Y\|195 - 299}	Y	195 - 299
24	X-RAY DIFFRACTION	24	{Z\|195 - 299}	Z	195 - 299

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