PDB-4hem: Llama vHH-02 binder of ORF49 (RBP) from lactococcal phage TP901-1

ID or keywords:

Entry

Database: PDB / ID: 4hem

Title

Llama vHH-02 binder of ORF49 (RBP) from lactococcal phage TP901-1

Components

Anti-baseplate TP901-1 Llama vHH 02
BPP

Keywords

VIRAL PROTEIN / Alpha-beta / Phage Receptor Binding Protein / Llama vHH / 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: 1.65 Å

Authors

Desmyter, A. / Spinelli, S. / Farenc, C. / Blangy, S. / Bebeacua, C. / van Sinderen, D. / Mahony, J. / 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	Oct 4, 2012	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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4hem_validation.pdf.gz	463.8 KB	Display	wwPDB validaton report
Full document	4hem_full_validation.pdf.gz	470.3 KB	Display
Data in XML	4hem_validation.xml.gz	38.8 KB	Display
Data in CIF	4hem_validation.cif.gz	57.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/4hem ftp://data.pdbj.org/pub/pdb/validation_reports/he/4hem	HTTPS FTP

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Related structure data

Related structure data	4hepC 4iosC 3hg0S 2f0c S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5k31-3 5b3d-d 5e7f-d 5k31-1 5k31-2 6m76-d 4ak3-1 1tei-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
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #132 - Dec 2010 Adenovirus similarity (1)

Deposited unit

A: BPP

B: BPP

C: BPP

E: Anti-baseplate TP901-1 Llama vHH 02

F: Anti-baseplate TP901-1 Llama vHH 02

G: Anti-baseplate TP901-1 Llama vHH 02

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	70.980, 104.250, 122.180
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	BPP / Baseplate protein Mass: 17165.240 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus phage TP901-1 (virus) / Gene: bpp, orf49 / Plasmid: pETG201 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9G096
#2: Antibody	Anti-baseplate TP901-1 Llama vHH 02 Mass: 13750.020 Da / Num. of mol.: 3 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.44 Å³/Da / Density % sol: 49.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEG 4000, 0.2M ammonium sulfate, 0.1M Na acetate, 4.7 mg/ml Protein complex , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Sep 19, 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: 1.65→48 Å / Num. all: 108049 / Num. obs: 108049 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / B_iso Wilson estimate: 25.49 Å² / R_merge(I) obs: 0.054 / Net I/σ(I): 26
Reflection shell	Resolution: 1.65→1.69 Å / Redundancy: 15 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 5.7 / Num. unique all: 7798 / % possible all: 97.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3HG0

3hg0

Resolution: 1.65→24.16 Å / Cor.coef. F_o:F_c: 0.9546 / Cor.coef. F_o:F_c free: 0.9511 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU R_free Blow DPI: 0.077 / SU R_free Cruickshank DPI: 0.073 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1772	3234	2.99 %	RANDOM
R_work	0.1674	-	-	-
all	0.1677	108009	-	-
obs	0.1677	108009	98.7 %	-

Displacement parameters

B_iso max: 136.88 Å² / B_iso mean: 31.64 Å² / B_iso min: 14.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.5781 Å²	0 Å²	0 Å²
2-	-	-8.4038 Å²	0 Å²
3-	-	-	3.8257 Å²

Refine analyze

Luzzati coordinate error obs: 0.18 Å

Refinement step

Cycle: LAST / Resolution: 1.65→24.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5745	0	0	921	6666

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	5971	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.09	8121	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d	0	1999	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	0	135	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	0	902	HARMONIC	5
X-RAY DIFFRACTION	t_it	0	5971	HARMONIC	20
X-RAY DIFFRACTION	t_omega_torsion	4.36
X-RAY DIFFRACTION	t_other_torsion	14.77
X-RAY DIFFRACTION	t_chiral_improper_torsion	0	777	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact	0	7462	SEMIHARMONIC	4

LS refinement shell

Resolution: 1.65→1.69 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2163	205	2.63 %
R_work	0.1792	7577	-
all	0.1802	7782	-
obs	-	-	98.7 %

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	0.0149	0.0439	0.204	0.0015	0.1037	0.066	-0.0001	-0.0004	0.0006	0.0014	0.0008	-0.0045	0.0037	0.0002	-0.0007	0.0064	-0.0089	-0.0097	0.009	-0.0324	-0.0145	9.3152	-35.0988	-19.5331
2	0.0115	0.0578	0.0925	0.0001	-0.0162	0.1153	0.0001	-0.0006	0.0022	0.0022	0.0008	-0.0053	0.002	0.0017	-0.0008	-0.0146	-0.008	-0.0389	0.0125	-0.0301	0.0038	18.4248	-31.7139	-9.3746
3	0.195	-0.2026	-0.1061	0.0349	0.1864	0.0015	-0.001	-0.0159	0.0048	-0.0071	0.0013	0.0157	0.0096	-0.0117	-0.0004	-0.0011	0.015	0.0275	-0.0055	-0.0419	0.0112	5.9014	-14.0538	0.0159
4	0.9119	0.2234	0.2068	0.1703	0.059	0.2531	0.0045	-0.0349	-0.0291	0.0009	0.0026	-0.0062	0.0013	-0.0091	-0.0071	-0.0207	0.0204	0.02	0.0026	-0.0293	0.0047	5.7567	-8.7721	11.8256
5	0.1832	0.1719	0.1157	0.0896	0.3798	0.4756	0.005	-0.0129	0.0067	0.0041	-0.0024	0.0035	-0.0021	-0.0066	-0.0026	-0.0058	0.0323	0.0002	-0.0091	-0.0198	0.0098	11.6083	-1.9904	12.5257
6	0.4388	0.0894	-0.0077	0.0643	0.0189	0.049	0.0031	-0.0225	0.0011	0.0083	-0.0035	0.0061	-0.0017	-0.0012	0.0004	-0.0163	0.0328	0.0318	0.0016	-0.0364	0.014	8.5817	-1.6397	11.158
7	0.391	-0.1964	0.2154	0	-0.0068	0.0668	0.0002	0.0022	0.0107	0.0011	-0.0033	0.0054	-0.0021	-0.0011	0.0031	-0.0283	0.0251	0.0226	0.0173	-0.0094	0.0102	-25.0412	4.8009	5.9713
8	0.2505	-0.2133	0.0844	0.0015	0.2503	0	-0.0016	0.0089	0.016	-0.0073	0.0059	0.0026	0.0042	-0.0071	-0.0043	-0.0276	0.0301	0.0314	0.0258	-0.0009	0.0035	-16.4982	-1.8166	-1.5097
9	0.3106	0.2101	-0.4482	0.0265	0.0841	0.0335	-0.0014	0.0099	0.0062	-0.0017	-0.0004	-0.0023	-0.003	-0.0059	0.0019	-0.0352	0.005	0.0341	-0.005	-0.0455	0.0372	-11.1235	1.7028	7.2929
10	0.932	-0.3471	-0.4752	0.0258	0.4915	0.0127	-0.0009	0.0105	0.0159	0.008	0.0059	-0.0015	-0.0009	-0.0104	-0.005	-0.0349	-0.0066	0.0189	0.0288	-0.0444	-0.0036	-18.36	-2.9133	8.6363
11	0.2065	-0.2909	-0.2407	0	-0.2536	0.0285	0.0001	0.0006	0.022	0.0124	-0.0132	-0.0059	-0.0063	-0.0004	0.0131	-0.0405	0.0374	0.0547	0.0107	-0.0234	0.0282	-19.0569	6.2204	10.3209
12	0.4527	0.2692	0.0002	0.362	-0.2091	0	0.0012	0.0082	0.0028	0.0008	-0.006	-0.0071	-0.0167	-0.0036	0.0048	-0.0555	0.044	0.0283	0.005	0.0305	0.0411	-12.1823	5.6204	3.2448
13	0.0542	-0.0393	-0.0698	0	0.0861	0.0626	0.0006	0.003	0.0011	-0.0033	-0.0012	-0.0022	0.0013	0.0027	0.0006	-0.011	-0.0027	-0.0073	0.0212	-0.0386	-0.0087	20.0106	-33.9601	-21.1375
14	0.1325	0.2275	0.0948	0.0379	0.0562	0.0244	-0.0002	0.0027	0.0009	0.0029	0.0003	-0.001	-0.001	0.0007	-0.0001	0.0005	-0.0173	-0.0131	0.0146	-0.0325	-0.0151	9.5341	-29.5116	-13.0263
15	0.0191	0.118	0.0426	0.1785	-0.1105	0.0516	0.0051	0.0207	-0.0026	-0.0075	0.0058	0.0011	-0.0424	-0.0146	-0.0109	0.0298	-0.003	-0.0236	-0.0454	-0.0147	0.0109	16.5225	-5.9774	-11.7407
16	0.4357	0.057	0.0772	0.3539	-0.0844	0.5092	0.0014	0.0309	-0.008	0.0051	0.0064	-0.0049	-0.0154	-0.0358	-0.0078	0.0286	0.009	-0.0167	-0.0427	-0.0013	-0.0031	10.1349	4.0896	-9.4149
17	0.0727	-0.1379	-0.2185	0.0913	-0.0028	0.4396	0.0014	0.0054	0.0053	0.0033	0.0004	-0.0002	-0.0188	-0.0084	-0.0018	0.0195	0.012	-0.0197	-0.012	-0.0087	-0.0103	9.798	6.1376	-0.5717
18	0.233	-0.326	0.4546	0.2075	-0.35	0.3338	0.0012	0.0077	0.0029	0.0067	0.0058	-0.0026	-0.0252	-0.0224	-0.007	0.02	-0.0006	-0.0259	-0.036	-0.0115	0.0105	11.7832	6.5681	-2.6021
19	0.1269	0.079	-0.1541	0.0055	-0.1183	0	-0.0008	-0.0012	0.0018	-0.0036	0.0011	-0.0002	-0.0034	0.0063	-0.0003	0.0071	-0.0232	0.0172	-0.004	0.0111	0.0006	37.0299	20.8396	-21.1924
20	0.0544	0.1812	-0.4653	0.0857	0.0448	0	0.0001	0.0028	0.0014	0.0017	-0.0035	-0.0021	-0.0001	0.0156	0.0034	0.0099	-0.0199	0.0341	-0.0057	-0.0008	0	35.5525	9.2123	-17.3329
21	0.0006	0.2966	-0.2489	0.1496	-0.4791	0.3265	-0.001	-0.0026	0.0041	-0.007	0.0013	-0.0018	0.0071	0.0045	-0.0003	0.0357	-0.0409	0.0044	-0.031	0.0016	-0.0086	26.849	14.7511	-13.8792
22	0	0.1434	-0.4596	0.1892	-0.4289	0.0388	-0.0031	0.0074	0.0052	-0.0084	0.0007	0.0006	-0.0014	0.0049	0.0024	0.0311	-0.0293	0.026	-0.0136	0.0052	-0.0142	28.3271	15.6974	-21.686
23	0.0201	0.0219	-0.2902	0.0983	-0.2857	0.0482	-0.0009	-0.0098	0.0081	-0.006	-0.0024	0.0031	-0.0072	0.0007	0.0033	0.0202	-0.0434	0.008	-0.0158	0.0183	-0.0021	30.6386	23.1587	-17.1079
24	0.0883	0.0893	0.1492	0.0726	-0.0587	0.3537	0.0001	-0.0117	0.0035	-0.0062	0.0007	-0.005	-0.0002	0.007	-0.0008	0.005	-0.0385	0.0088	-0.0066	0.0219	0	32.1439	15.4826	-10.7734
25	0.0437	-0.0085	0.0007	0.0014	-0.0472	0.0408	0.0001	-0.0019	-0.001	-0.0028	-0.0005	-0.0048	0.0001	-0.0015	0.0004	-0.0075	0.0153	-0.0271	0.0097	-0.0323	-0.0018	16.448	-39.4442	-12.4509
26	0.0136	0.0398	0.0176	0.0276	0.009	0.0583	-0.0007	0.0007	-0.0017	-0.001	0.0018	-0.0038	-0.0032	0.0029	-0.0011	-0.0078	-0.0129	-0.0089	0.0092	-0.0126	0.0009	17.5532	-26.5616	-17.7631
27	0.0181	0.2796	0.1524	0	0.2961	0.2886	-0.0002	0.011	-0.0064	0.0052	-0.0028	-0.0086	-0.0035	-0.0016	0.003	0.009	-0.0024	-0.034	0.008	-0.0477	-0.0071	23.9122	-14.5865	2.754
28	0.1587	-0.1392	0.0328	0.4101	-0.3826	0.5919	0.005	0.0265	0.0133	-0.0169	-0.0173	-0.0142	0.0081	0.0126	0.0123	-0.0041	-0.0001	-0.0058	0.0187	-0.0346	-0.0292	29.5761	-3.7682	4.8428
29	0.3454	0.0402	0.2759	0.3159	-0.1866	0.1403	-0.0046	-0.0035	0.0111	-0.0111	-0.0031	-0.0074	-0.0028	-0.0012	0.0077	0.006	0.0127	-0.0006	0.0129	-0.0238	-0.025	24.1268	2.9097	4.5898
30	0.3712	0.2052	-0.1326	0.144	-0.0743	0.1103	0.0008	0.0062	0.013	0.0041	-0.007	-0.016	-0.007	0.0049	0.0062	0.0064	0.0073	-0.0237	0.0127	-0.046	-0.02	24.6906	1.1439	7.0195
31	0.0083	0.1295	-0.078	0.0045	-0.2341	0.3795	-0.001	-0.0089	-0.0043	0.0075	0.004	0.004	-0.0025	0.0089	-0.003	-0.0002	0.004	-0.0156	0.0205	-0.0009	-0.0221	34.7928	-15.167	35.907
32	0	0.0878	-0.0872	0.0534	-0.2367	0.4955	-0.0016	-0.0104	-0.0267	0.0078	0.0052	0.0057	-0.0108	-0.0095	-0.0036	0.007	0.0073	0.0077	-0.0094	-0.0252	-0.0023	28.1062	-19.939	26.4012
33	0.3619	-0.161	0.278	0.236	-0.2131	0.142	-0.0009	0.0029	-0.0082	-0.0004	0.0033	0.0006	-0.0068	-0.0031	-0.0024	0.0202	0.0283	0.0058	0.0057	-0.042	-0.0292	30.5817	-8.4873	24.5864
34	0.1193	-0.0733	0.2037	0	0.0021	0.6257	-0.0013	-0.0084	-0.0174	0.0022	-0.0001	0.0037	-0.0093	0.0202	0.0014	0.0195	0.0111	-0.0038	-0.017	-0.027	-0.0061	36.948	-13.7591	26.051
35	0.1584	-0.0309	0.0303	0.1032	-0.124	0.4826	0.0016	-0.0024	0.0012	0.0166	0.0092	0.0026	-0.0234	0.0019	-0.0107	0.0179	0.0218	0.0092	0.0287	-0.0469	-0.0473	34.4895	-8.0437	32.8692
36	0.4402	-0.147	-0.3396	0.1601	0.0717	0.3147	-0.0005	-0.0036	-0.0009	0.0182	0.0115	0.0175	-0.0039	-0.0069	-0.011	-0.0037	0.0261	0.0086	0.0301	0.0002	-0.034	25.566	-10.3093	27.4863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{A\|34 - A\|43}	A	34 - 43
2	X-RAY DIFFRACTION	2	{A\|44 - A\|53}	A	44 - 53
3	X-RAY DIFFRACTION	3	{A\|54 - A\|78}	A	54 - 78
4	X-RAY DIFFRACTION	4	{A\|79 - A\|116}	A	79 - 116
5	X-RAY DIFFRACTION	5	{A\|117 - A\|143}	A	117 - 143
6	X-RAY DIFFRACTION	6	{A\|144 - A\|163}	A	144 - 163
7	X-RAY DIFFRACTION	7	{G\|1 - G\|20}	G	1 - 20
8	X-RAY DIFFRACTION	8	{G\|21 - G\|38}	G	21 - 38
9	X-RAY DIFFRACTION	9	{G\|39 - G\|60}	G	39 - 60
10	X-RAY DIFFRACTION	10	{G\|61 - G\|80}	G	61 - 80
11	X-RAY DIFFRACTION	11	{G\|81 - G\|100}	G	81 - 100
12	X-RAY DIFFRACTION	12	{G\|101 - G\|123}	G	101 - 123
13	X-RAY DIFFRACTION	13	{B\|34 - B\|43}	B	34 - 43
14	X-RAY DIFFRACTION	14	{B\|44 - B\|53}	B	44 - 53
15	X-RAY DIFFRACTION	15	{B\|54 - B\|78}	B	54 - 78
16	X-RAY DIFFRACTION	16	{B\|79 - B\|116}	B	79 - 116
17	X-RAY DIFFRACTION	17	{B\|117 - B\|143}	B	117 - 143
18	X-RAY DIFFRACTION	18	{B\|144 - B\|163}	B	144 - 163
19	X-RAY DIFFRACTION	19	{E\|1 - E\|20}	E	1 - 20
20	X-RAY DIFFRACTION	20	{E\|21 - E\|38}	E	21 - 38
21	X-RAY DIFFRACTION	21	{E\|39 - E\|60}	E	39 - 60
22	X-RAY DIFFRACTION	22	{E\|61 - E\|80}	E	61 - 80
23	X-RAY DIFFRACTION	23	{E\|81 - E\|100}	E	81 - 100
24	X-RAY DIFFRACTION	24	{E\|101 - E\|123}	E	101 - 123
25	X-RAY DIFFRACTION	25	{C\|34 - C\|43}	C	34 - 43
26	X-RAY DIFFRACTION	26	{C\|44 - C\|53}	C	44 - 53
27	X-RAY DIFFRACTION	27	{C\|54 - C\|78}	C	54 - 78
28	X-RAY DIFFRACTION	28	{C\|79 - C\|116}	C	79 - 116
29	X-RAY DIFFRACTION	29	{C\|117 - C\|143}	C	117 - 143
30	X-RAY DIFFRACTION	30	{C\|144 - C\|163}	C	144 - 163
31	X-RAY DIFFRACTION	31	{F\|1 - F\|20}	F	1 - 20
32	X-RAY DIFFRACTION	32	{F\|21 - F\|38}	F	21 - 38
33	X-RAY DIFFRACTION	33	{F\|39 - F\|60}	F	39 - 60
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35	X-RAY DIFFRACTION	35	{F\|81 - F\|100}	F	81 - 100
36	X-RAY DIFFRACTION	36	{F\|101 - F\|122}	F	101 - 122

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