PDB-5bop: Crystal structure of the artificial nanobody octarellinV.1 complex

ID or keywords:

Entry

Database: PDB / ID: 5bop

Title

Crystal structure of the artificial nanobody octarellinV.1 complex

Components

Nanobody
Octarellin V.1

Keywords

DE NOVO PROTEIN / synthetic gene / artificial protein / Rossmann-like

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Lama glama (llama)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.95 Å

Authors

Figueroa, M. / Sleutel, M. / Pardon, E. / Steyaert, J. / Martial, J.A. / van de Weerdt, C.

Citation

Journal: J.Struct.Biol. / Year: 2016
Title: The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.
Authors: Figueroa, M. / Sleutel, M. / Vandevenne, M. / Parvizi, G. / Attout, S. / Jacquin, O. / Vandenameele, J. / Fischer, A.W. / Damblon, C. / Goormaghtigh, E. / Valerio-Lepiniec, M. / Urvoas, A. / ...

History

Deposition	May 27, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	May 25, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 8, 2016	Group: Database references
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5bop.cif.gz	247.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5bop.ent.gz	201.1 KB	Display	PDB format
PDBx/mmJSON format	5bop.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5bop_validation.pdf.gz	447.3 KB	Display	wwPDB validaton report
Full document	5bop_full_validation.pdf.gz	449.5 KB	Display
Data in XML	5bop_validation.xml.gz	23.7 KB	Display
Data in CIF	5bop_validation.cif.gz	33.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/5bop ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bop	HTTPS FTP

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Related structure data

Related structure data	4zv6C C: citing same article (ref.)
Similar structure data	6rbt-d 6rc0-d 6rc1-d 6rc4-d 6rbx-d 5a7z-d 4dx1-2 6rbp-d 6rc2-d 2gq0-1 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Nanobody

B: Octarellin V.1

C: Nanobody

D: Octarellin V.1

79.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nanobody

B: Octarellin V.1

defined by author&software
39.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Nanobody

D: Octarellin V.1

defined by author&software
39.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.920, 62.860, 95.110
Angle α, β, γ (deg.)	90.00, 96.22, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Antibody	Nanobody Mass: 14863.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#2: Protein	Octarellin V.1 Mass: 24867.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pJB122 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.05 Å³/Da / Density % sol: 40.11 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris pH 8.5, 22% PEG 3350, 10% EtOH, streak seeding

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 1.95→8.72 Å / Num. obs: 89920 / % possible obs: 97.5 % / Redundancy: 2.3 % / Net I/σ(I): 8.51

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Resolution: 1.95→8.72 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2292	2352	5 %
R_work	0.1921	-	-
obs	0.194	47033	99.68 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→8.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4553	0	0	247	4800

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4646
X-RAY DIFFRACTION	f_angle_d	1.012	6246
X-RAY DIFFRACTION	f_dihedral_angle_d	14.155	1692
X-RAY DIFFRACTION	f_chiral_restr	0.048	647
X-RAY DIFFRACTION	f_plane_restr	0.005	825

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 (%)
1.95-1.9898	0.4111	138	0.371	2621	X-RAY DIFFRACTION	100
1.9898-2.0331	0.3863	139	0.3371	2636	X-RAY DIFFRACTION	100
2.0331-2.0804	0.3502	136	0.3037	2595	X-RAY DIFFRACTION	100
2.0804-2.1324	0.3035	137	0.2753	2599	X-RAY DIFFRACTION	100
2.1324-2.19	0.3172	139	0.2461	2624	X-RAY DIFFRACTION	100
2.19-2.2545	0.2772	138	0.2473	2635	X-RAY DIFFRACTION	100
2.2545-2.3273	0.2693	136	0.2203	2597	X-RAY DIFFRACTION	99
2.3273-2.4104	0.2735	136	0.2277	2589	X-RAY DIFFRACTION	100
2.4104-2.5069	0.2534	139	0.2138	2636	X-RAY DIFFRACTION	99
2.5069-2.621	0.2608	138	0.2067	2613	X-RAY DIFFRACTION	99
2.621-2.7592	0.2635	137	0.2007	2611	X-RAY DIFFRACTION	99
2.7592-2.9321	0.243	137	0.1992	2607	X-RAY DIFFRACTION	100
2.9321-3.1584	0.2121	140	0.1895	2647	X-RAY DIFFRACTION	100
3.1584-3.4762	0.2122	140	0.1743	2657	X-RAY DIFFRACTION	100
3.4762-3.979	0.1788	139	0.1603	2641	X-RAY DIFFRACTION	100
3.979-5.0124	0.1594	139	0.1411	2659	X-RAY DIFFRACTION	100
5.0124-49.6833	0.2223	144	0.1698	2714	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	1.7982	-1.7732	-0.4181	6.8617	-0.8546	2.6772	-0.3414	-0.3522	-0.3639	0.2564	0.5402	0.376	0.546	-0.2256	-0.1252	0.3536	-0.0909	0.0881	0.2661	0.027	0.2586	16.8846	29.289	73.1548
2	3.2343	-1.1746	-0.4123	3.8959	-0.6376	3.8023	0.063	0.2005	0.0105	-0.3075	0.0074	-0.2746	0.5751	0.1224	-0.0606	0.3201	-0.0544	0.0593	0.1618	-0.0243	0.2225	20.1561	30.3577	62.9445
3	6.6883	-3.4728	-1.5314	2.5382	3.3515	9.4712	0.192	0.2577	-0.1108	-0.0586	0.3007	0.3619	0.398	-0.8089	-0.5474	0.3529	-0.1053	0.0361	0.2343	0.0885	0.2914	11.5595	28.1004	67.7191
4	2.0125	-1.5265	0.1587	1.5693	-1.8985	3.3772	0.004	0.0421	-0.2064	-0.4094	-0.2224	-0.2064	0.7123	0.1515	0.1961	0.3187	-0.0319	0.0643	0.1628	-0.0276	0.2104	22.775	30.4412	66.5226
5	4.0604	-0.388	0.1793	5.81	-0.278	6.901	0.0929	-0.1474	0.345	0.3312	0.1137	-0.1297	-1.161	0.2371	-0.1865	0.4193	-0.0691	0.1021	0.1539	0.0012	0.2298	13.7802	56.839	62.0431
6	8.9642	1.2033	-3.7325	4.6	-1.3216	8.6006	0.0477	0.9363	1.4615	-1.434	0.6677	1.5096	-0.9315	-1.8444	-0.8059	0.8208	0.2479	-0.1407	0.5978	0.1382	0.6891	1.5834	62.1623	48.1165
7	4.9297	3.6019	-3.0431	1.84	-2.1654	3.6388	0.6758	0.3753	0.3488	-0.3776	-0.2812	0.1778	-1.1661	-0.0735	-0.3844	0.6614	-0.0305	0.125	0.2728	0.0447	0.2223	15.197	62.4161	49.4921
8	4.0157	-1.1488	-2.2242	6.1513	-2.028	4.9245	0.006	0.4675	-0.2399	-0.7206	-0.1192	0.0124	-0.0584	-0.0358	0.107	0.3843	-0.0528	-0.0002	0.2421	-0.0042	0.1424	12.624	50.8569	52.6474
9	2.1573	1.2902	-0.2241	3.6617	0.2365	1.6903	-0.202	0.3956	-0.2032	-0.691	0.2306	0.33	0.1077	-0.2225	-0.0436	0.2439	-0.0147	-0.0776	0.2558	-0.0115	0.2373	-12.318	32.0824	70.8713
10	6.486	3.1714	-0.9756	5.8355	0.7149	3.7056	-0.0824	-0.1122	0.1064	-0.1057	-0.0248	0.3833	0.1441	-0.1696	0.0495	0.155	0.0286	-0.0004	0.1356	0.0081	0.1298	-8.6199	35.2577	80.2309
11	7.1388	3.6836	-4.1023	2.9162	-4.2121	8.4607	0.0274	0.1817	-0.2085	0.1073	0.1672	-0.229	-0.3108	0.162	0.0282	0.254	0.0216	0.0144	0.257	-0.0281	0.2387	-4.1215	30.9432	72.9108
12	1.398	1.2528	-0.0661	3.9209	1.9585	1.8218	-0.0491	-0.0008	-0.0262	-0.1438	-0.2903	1.0143	0.102	-0.2678	0.3163	0.1399	0.0014	-0.0565	0.2464	-0.021	0.3552	-14.958	33.9952	75.9865
13	4.8494	-1.4389	-0.3887	6.1669	0.6136	7.7266	0.1878	0.1099	0.3019	-0.7871	0.0388	0.1921	-0.5519	-0.2825	-0.2531	0.3302	-0.0026	0.034	0.1532	-0.0019	0.2328	-3.6746	58.6365	79.3461
14	5.2968	-0.081	-2.3571	3.0267	-1.2516	2.527	0.0081	-0.7197	0.7027	0.6155	0.6643	-1.2317	-0.3582	1.2041	-0.5162	0.4944	-0.2289	0.108	0.5845	-0.3041	0.7885	11.1447	64.5014	90.1997
15	4.6731	-3.5143	-3.2236	3.1335	2.3801	7.5226	0.4903	-0.2403	0.6273	-0.0325	0.0999	-0.4398	-1.3254	0.2504	-0.5434	0.4479	-0.0541	0.132	0.2309	-0.0749	0.2917	-2.6835	65.9296	90.9723
16	4.002	-0.5888	-1.0743	6.337	1.697	4.5347	-0.0972	-0.5261	-0.0056	0.4617	0.1018	0.1565	-0.1811	-0.0192	0.0105	0.2984	0.001	0.037	0.2479	-0.0061	0.1319	-1.368	53.9255	87.4935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:32)
2	X-RAY DIFFRACTION	2	(chain A and resid 33:64)
3	X-RAY DIFFRACTION	3	(chain A and resid 65:84)
4	X-RAY DIFFRACTION	4	(chain A and resid 85:124)
5	X-RAY DIFFRACTION	5	(chain B and resid 2:61)
6	X-RAY DIFFRACTION	6	(chain B and resid 62:82)
7	X-RAY DIFFRACTION	7	(chain B and resid 83:117)
8	X-RAY DIFFRACTION	8	(chain B and resid 118:192)
9	X-RAY DIFFRACTION	9	(chain C and resid 2:43)
10	X-RAY DIFFRACTION	10	(chain C and resid 44:64)
11	X-RAY DIFFRACTION	11	(chain C and resid 65:84)
12	X-RAY DIFFRACTION	12	(chain C and resid 85:124)
13	X-RAY DIFFRACTION	13	(chain D and resid 2:61)
14	X-RAY DIFFRACTION	14	(chain D and resid 62:82)
15	X-RAY DIFFRACTION	15	(chain D and resid 83:117)
16	X-RAY DIFFRACTION	16	(chain D and resid 118:193)

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