PDB-4ios: Structure of phage TP901-1 RBP (ORF49) in complex with nanobody 11.

ID or keywords:

Entry

Database: PDB / ID: 4ios

Title

Structure of phage TP901-1 RBP (ORF49) in complex with nanobody 11.

Components

BPP
Llama nanobody 11

Keywords

VIRAL PROTEIN / all beta / jelly roll motif / receptor binding protein / neutralizing llama antibody domain / CELL ADHESION-IMMUNE SYSTEM complex

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)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Desmyter, A. / Farenc, C. / Mahony, J. / Spinelli, S. / Bebeacua, C. / Blangy, S. / Veesler, D. / van Sinderen, D. / Cambillau, C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Viral infection modulation and neutralization by camelid nanobodies
Authors: Desmyter, A. / Farenc, C. / Mahony, J. / Spinelli, S. / Bebeacua, C. / Blangy, S. / Veesler, D. / van Sinderen, D. / Cambillau, C.

History

Deposition	Jan 8, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 31, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	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 / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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PDBx/mmCIF format	4ios.cif.gz	302.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4ios_validation.pdf.gz	495 KB	Display	wwPDB validaton report
Full document	4ios_full_validation.pdf.gz	512.1 KB	Display
Data in XML	4ios_validation.xml.gz	33.9 KB	Display
Data in CIF	4ios_validation.cif.gz	47.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/io/4ios ftp://data.pdbj.org/pub/pdb/validation_reports/io/4ios	HTTPS FTP

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Related structure data

Related structure data	4hemSC 4hepC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4f2g-3 3c19-1 6kxk-7 6jkr-1 2ef0-2 6ty6-d 5g1p-2 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)

Deposited unit

A: BPP

B: BPP

C: BPP

D: Llama nanobody 11

E: Llama nanobody 11

F: Llama nanobody 11

G: Llama nanobody 11

H: BPP

hetero molecules

95.5 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BPP

B: BPP

C: BPP

E: Llama nanobody 11

F: Llama nanobody 11

G: Llama nanobody 11

hetero molecules

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

2

D: Llama nanobody 11

H: BPP

D: Llama nanobody 11

H: BPP

D: Llama nanobody 11

H: BPP

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

Unit cell

Length a, b, c (Å)	148.280, 148.280, 104.590
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

#1: Protein	BPP / Baseplate protein Mass: 10551.824 Da / Num. of mol.: 4 / Fragment: head domain, residues 64-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, ORF49 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9G096
#2: Protein	Llama nanobody 11 Mass: 13300.686 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.32 Å³/Da / Density % sol: 46.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 20% PEG 1000, 0.2M Lithium Sulfate, 0.1M Na Phosphate Citrate, pH 4.2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.931 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2012
Radiation	Monochromator: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. all: 33444 / Num. obs: 33444 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / B_iso Wilson estimate: 56.87 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2.4→2.54 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.534 / Mean I/σ(I) obs: 2.25 / Num. unique all: 5342 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
MOLREP		phasing
BUSTER	2.11.2	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4HEM

4hem

Resolution: 2.4→22.01 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.9145 / Occupancy max: 1 / Occupancy min: 0.8 / SU R Cruickshank DPI: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2269	1672	5 %	RANDOM
R_work	0.2006	-	-	-
all	0.2019	33442	-	-
obs	0.2019	33442	99.9 %	-

Displacement parameters

B_iso mean: 54.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.3062 Å²	0 Å²	0 Å²
2-	-	-2.3062 Å²	0 Å²
3-	-	-	4.6123 Å²

Refine analyze

Luzzati coordinate error obs: 0.328 Å

Refinement step

Cycle: LAST / Resolution: 2.4→22.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6300	0	6	235	6541

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	2066	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	116	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	974	HARMONIC	5
X-RAY DIFFRACTION	t_it	6442	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	845	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	7047	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	6442	HARMONIC	2	0.009
X-RAY DIFFRACTION	t_angle_deg	8755	HARMONIC	2	1.21
X-RAY DIFFRACTION	t_omega_torsion				3.17
X-RAY DIFFRACTION	t_other_torsion				21.97

LS refinement shell

Resolution: 2.4→2.47 Å / Total num. of bins used: 17

	R_factor	Num. reflection	% reflection
R_free	0.2876	143	5.01 %
R_work	0.2314	2709	-
all	0.2344	2852	-
obs	-	-	99.9 %

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	0.1502	-0.0062	0.1487	-0.0572	-0.0062	0.0364	-0.0012	0.0003	-0.002	0.0005	0.0019	-0.0001	0.0011	0.0047	-0.0007	-0.0051	-0.0028	-0.0074	0.002	0.0003	0.0003	-23.5582	14.1287	-18.036
2	0.3065	-0.2431	0.3969	0.0318	0.0389	0.2937	-0.0015	0.0009	-0.0061	0.0014	0.0023	-0.0014	-0.0044	0.0197	-0.0008	-0.0089	0.0068	-0.0214	-0.0095	-0.0044	0.0108	-23.1204	13.5542	-23.5936
3	0.0762	0.1967	0.1184	0.2889	0.3666	0.0428	0.0014	-0.001	0.0048	-0.0005	0.0022	0.0028	0.0046	0.0161	-0.0036	-0.0035	-0.0092	-0.0385	-0.0168	-0.0115	0.0196	-27.5983	17.9677	-30.0685
4	0.2773	-0.0137	0.3281	-0.091	-0.0089	0.1916	-0.0008	0.0009	0.0022	0.0047	0.0027	-0.0018	-0.0007	0.0089	-0.0019	0.0112	-0.0189	-0.0116	-0.0236	-0.0067	0.0069	-27.922	18.1477	-27.1973
5	0.1063	-0.0546	-0.0286	-0.065	0.0432	0.0556	0.0013	-0.0008	0.0017	-0.0015	-0.0001	-0.0005	0.0011	-0.004	-0.0012	-0.0094	0.0138	-0.0308	0.0068	0.0244	-0.0079	-53.4249	11.7384	-25.4151
6	0.1449	0.0108	-0.7575	0.0949	-0.5818	0.6601	0.0002	-0.013	0.0106	0.0038	0.0008	-0.0084	0.007	-0.0061	-0.001	0.0059	0.0386	-0.0115	0.0059	0.0476	-0.0366	-48.6403	12.4236	-22.6048
7	0.2464	-0.2393	0.0145	0.1139	0.16	0.0912	0.0096	-0.0039	0.0062	-0.0086	-0.0067	-0.0098	-0.0057	-0.007	-0.0029	0.02	0.0132	-0.0198	-0.0078	0.0067	-0.0161	-42.3145	18.4186	-25.5327
8	0.4579	0.045	-0.2145	-0.0229	0.0498	0.3576	0.0022	-0.0018	0.0057	0.0007	0.0006	-0.0005	-0.0043	-0.0025	-0.0028	0.0204	0.0105	-0.0183	-0.0118	0.0297	-0.0075	-44.6147	17.3273	-26.8803
9	0.0637	0.0377	0.1066	0.0222	0.0642	0.0527	-0.002	0.0043	-0.0006	-0.0003	0.0026	0.0003	0.0027	0.0001	-0.0006	-0.0044	-0.006	-0.0107	0.0008	0.0163	0.0018	-31.8614	6.2218	-46.2042
10	0.2105	0.1249	-0.405	0.2184	0.1909	0.4106	0.0053	-0.0025	-0.0001	-0.0026	0.0006	-0.0066	0.0004	-0.0053	-0.0058	0.0143	-0.0173	-0.0185	-0.0238	0.0875	-0.0331	-36.7696	6.7752	-43.7299
11	-0.1221	0.0428	0.4572	0.2184	-0.4038	0.1843	-0.0048	0.0044	0.0043	0.0048	0.001	-0.0064	-0.0056	-0.0005	0.0037	0.0302	-0.0057	-0.0176	-0.0233	0.0363	-0.0111	-39.2857	14.4209	-39.8912
12	0.2898	0.0729	0.2907	0.1647	0.0637	0.4011	0.0034	-0.0053	0.0056	0.0012	-0.0051	-0.0012	-0.0036	-0.0066	0.0017	0.0176	-0.003	-0.029	-0.0043	0.0491	-0.0196	-36.7518	13.8293	-40.7263
13	0.2504	-0.1193	0.1275	0.0452	0.0213	0.1134	-0.0012	0.0067	0.0021	-0.0027	-0.0023	-0.0057	-0.0034	0.0044	0.0035	-0.001	0.0067	-0.0075	0.0214	0.0197	0.0189	-36.3545	30.6237	-62.1703
14	0.0107	-0.0084	0.0022	-0.0031	-0.1023	0	0.0003	0.0024	-0.007	-0.0008	0	-0.0033	0.0026	0.0018	-0.0002	-0.0154	0.0039	0.0072	0.001	0.0178	0.0121	-46.0263	30.325	-67.6213
15	0.5971	-0.2962	-0.0481	-0.0838	-0.0194	0	0.0011	-0.0023	-0.0085	0.001	0.0008	-0.0061	0.0031	-0.0006	-0.0019	-0.0201	0.0104	-0.0052	0.009	0.0363	0.0057	-48.6212	36.5075	-65.4576
16	0.1061	-0.0674	-0.0472	-0.0847	-0.1497	0	-0.0011	0.0034	-0.0023	-0.0006	0.0012	-0.0027	-0.0017	0.0026	-0.0001	-0.0092	0.0028	-0.0045	-0.0051	0.0179	0.0004	-42.2816	38.27	-66.2953
17	0.1773	-0.0798	0.0691	-0.1342	-0.1215	0	-0.0001	-0.003	-0.006	0.0045	-0.0024	-0.0037	0.0004	0.0001	0.0026	-0.012	0.0011	-0.0131	-0.0008	0.0409	0.0049	-42.0199	33.8425	-59.1732
18	-0.0787	0.3901	0.0507	0.4767	-0.6541	0	-0.0009	0.0025	-0.0104	0.0041	-0.007	0.0001	-0.0002	-0.0004	0.0079	0.0025	0.001	-0.006	-0.0119	0.0426	0.0063	-50.2443	30.2387	-65.6656
19	-0.0184	0.011	0.0399	0.0188	0.0388	0.1384	0.0006	-0.0001	0.0037	-0.0002	0.0003	-0.0031	-0.0033	0	-0.0009	0.0082	0.0024	-0.0172	-0.002	-0.0239	-0.0031	-28.884	33.3255	4.1753
20	0.1016	-0.0307	0.1379	-0.0571	0.0413	0.0028	-0.0026	-0.0012	0.0033	0.0028	0.0016	0.0034	0.0007	-0.0007	0.001	-0.0039	0.0049	-0.0161	-0.005	-0.0231	0.0002	-33.672	23.5419	-1.818
21	-0.2033	0.1788	0.3877	0.3054	0.62	0.4207	-0.0022	0.0013	0.0039	0.0059	0.0051	0.0022	0.0018	-0.0042	-0.0029	0.0089	0.0024	-0.0472	-0.0164	-0.0333	-0.0031	-29.362	25.0396	-7.3933
22	-0.237	0.1852	0.2112	0.2929	0.1603	0.0605	-0.0011	-0.0023	0.0068	-0.0011	0.0031	-0.0015	-0.0027	0.0022	-0.0019	0.0066	-0.0016	-0.0371	-0.008	-0.0223	-0.0053	-24.985	24.3709	-1.5265
23	0.1329	-0.0062	0.2604	0.0739	0.0353	0.0069	0.0023	-0.0003	0.0031	-0.0015	-0.0027	-0.0026	-0.0005	0.0004	0.0004	-0.0003	0.0012	-0.0297	-0.0114	-0.0201	0.0102	-28.9253	33.7881	-2.8325
24	0.5296	-0.184	0.3877	-0.0696	0.0998	0.0139	-0.0004	-0.0008	0.0031	0.001	0.0038	0.0041	-0.0035	-0.0028	-0.0034	-0.0031	-0.0001	-0.0357	-0.0169	-0.0385	0.0133	-35.5988	25.6739	-6.306
25	0.2817	-0.0951	-0.1001	-0.2037	-0.1251	0	-0.0004	-0.001	-0.0002	-0.0016	0.0025	-0.0034	-0.0015	0.0024	-0.0021	-0.0106	-0.001	0.004	0.0082	0.0017	-0.0014	-7.9438	15.8768	-61.0446
26	0.0064	0.0099	0.0542	0.0093	0.0706	0.0749	-0.0005	-0.0016	0.0018	0.0012	0.0001	-0.0019	0.0007	0.0068	0.0003	-0.0008	-0.0006	0.0003	0.0011	-0.0096	-0.0007	-11.7304	11.5229	-49.5818
27	0.3382	-0.0843	-0.0188	-0.1083	-0.0293	0.1116	0.0007	-0.0007	-0.0027	0	0.0014	-0.0021	-0.0019	0.0055	-0.0021	0.0017	-0.0095	0.0069	-0.0066	-0.0044	0.0034	-18.7145	13.3899	-50.944
28	-0.0226	0.053	-0.0545	0.0687	-0.0237	0	0.0006	-0.0009	-0.0005	0.0001	0.0005	-0.0002	0.0025	0.005	-0.0011	-0.0067	-0.009	0.0038	-0.0004	-0.006	-0.002	-17.0127	10.0352	-56.9114
29	-0.0309	0.0767	0.0016	0.0988	-0.0054	0.0177	-0.0029	0.0006	0.0019	-0.0004	0.0039	-0.0016	-0.0036	0.0046	-0.001	0.0061	-0.0148	-0.0029	-0.0117	-0.0143	-0.0034	-13.5595	18.2814	-57.2303
30	0.0224	0.3636	0.4609	0.4124	0.3057	0.1865	-0.0073	-0.0018	0.0015	0.0053	0.0069	0.0003	-0.0011	0.0069	0.0004	-0.0008	-0.0206	-0.0147	-0.0064	-0.0063	-0.0016	-14.004	14.7716	-46.7097
31	0.0961	-0.0631	0.1564	-0.0698	0.0276	0.0572	-0.0014	0.0024	0.0015	-0.0003	0.0032	0.0017	-0.0039	-0.0021	-0.0018	-0.0161	0.0124	0.0003	0.0219	0.0109	-0.0061	-75.2789	19.9656	-44.5105
32	-0.0053	0.003	-0.0846	0.0053	-0.0603	0	0.0018	0.0056	-0.006	-0.0043	-0.0012	0.0008	-0.0001	-0.0052	-0.0005	-0.0211	0.0078	-0.0039	0.0318	0.0127	-0.0111	-64.7344	11.2312	-43.4506
33	0.5987	-0.2694	0.0618	-0.1945	0.0139	0.0499	-0.001	0.004	-0.0013	-0.0028	0.0004	0.0021	-0.0009	-0.0037	0.0006	-0.0276	0.0254	0.0002	0.0324	0.0337	-0.0093	-62.5042	15.7397	-37.9339
34	0.08	-0.048	0.1107	-0.0181	-0.1152	0.0024	0.0019	0.0018	-0.0037	-0.002	-0.0005	0.003	-0.0006	-0.0033	-0.0014	-0.0187	0.0152	-0.0007	0.0209	0.019	-0.0025	-69.3455	14.3489	-35.9899
35	0.1554	-0.0966	-0.0205	-0.1315	-0.0717	0.1265	-0.002	0.0045	0.003	0.0013	0.001	0.0018	-0.004	-0.0006	0.001	-0.0218	0.0201	0.0107	0.0304	0.0232	-0.0162	-68.6767	22.0361	-42.1538
36	0.4991	-0.2881	-0.725	-0.4991	-0.4727	0.4871	-0.0032	0.0066	-0.0065	0.0001	0.0027	0.0006	-0.0018	-0.0022	0.0006	-0.0211	0.0203	-0.004	0.0391	0.0378	-0.0261	-60.0243	14.0192	-43.9084

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|64 - A\|78}	A	64 - 78
2	X-RAY DIFFRACTION	2	{A\|79 - A\|116}	A	79 - 116
3	X-RAY DIFFRACTION	3	{A\|117 - A\|143}	A	117 - 143
4	X-RAY DIFFRACTION	4	{A\|144 - A\|163}	A	144 - 163
5	X-RAY DIFFRACTION	5	{B\|65 - B\|78}	B	65 - 78
6	X-RAY DIFFRACTION	6	{B\|79 - B\|116}	B	79 - 116
7	X-RAY DIFFRACTION	7	{B\|117 - B\|143}	B	117 - 143
8	X-RAY DIFFRACTION	8	{B\|144 - B\|163}	B	144 - 163
9	X-RAY DIFFRACTION	9	{C\|65 - C\|78}	C	65 - 78
10	X-RAY DIFFRACTION	10	{C\|79 - C\|116}	C	79 - 116
11	X-RAY DIFFRACTION	11	{C\|117 - C\|143}	C	117 - 143
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