PDB-5m14: Synthetic nanobody in complex with MBP

ID or keywords:

Entry

Database: PDB / ID: 5m14

Title

Synthetic nanobody in complex with MBP

Components

Maltose-binding periplasmic protein
synthetic Nanobody L2_G11 (a-MBP#2)

Keywords

IMMUNE SYSTEM / nanobody synthetic library / maltose bidning protein

Function / homology

Function and homology information

detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Zimmermann, I. / Egloff, P. / Seeger, M.A.

Citation

Journal: Elife / Year: 2018
Title: Synthetic single domain antibodies for the conformational trapping of membrane proteins.
Authors: Zimmermann, I. / Egloff, P. / Hutter, C.A. / Arnold, F.M. / Stohler, P. / Bocquet, N. / Hug, M.N. / Huber, S. / Siegrist, M. / Hetemann, L. / Gera, J. / Gmur, S. / Spies, P. / Gygax, D. / ...

History

Deposition	Oct 7, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 16, 2019	Group: Data collection / Category: reflns_shell

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5m14.cif.gz	407.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5m14.ent.gz	345.8 KB	Display	PDB format
PDBx/mmJSON format	5m14.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5m14_validation.pdf.gz	447.4 KB	Display	wwPDB validaton report
Full document	5m14_full_validation.pdf.gz	452.2 KB	Display
Data in XML	5m14_validation.xml.gz	45.6 KB	Display
Data in CIF	5m14_validation.cif.gz	68.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m1/5m14 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m14	HTTPS FTP

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Related structure data

Related structure data	5m13C 5m15C C: citing same article (ref.)
Similar structure data	4gqs-1 6dwm-2 1y4c-d 1efp-2 1efp-1 6vlt-8 4ejg-4 1i6x-d 1og2-1 3ibd-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5m13C

5m15C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (6) #221 - May 2018 Human Papillomavirus and Vaccines similarity (6) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (6) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Maltose-binding periplasmic protein

B: Maltose-binding periplasmic protein

C: synthetic Nanobody L2_G11 (a-MBP#2)

D: synthetic Nanobody L2_G11 (a-MBP#2)

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

1

A: Maltose-binding periplasmic protein

C: synthetic Nanobody L2_G11 (a-MBP#2)

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

2

D: synthetic Nanobody L2_G11 (a-MBP#2)

B: Maltose-binding periplasmic protein

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

3

B: Maltose-binding periplasmic protein

D: synthetic Nanobody L2_G11 (a-MBP#2)

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

Unit cell

Length a, b, c (Å)	57.890, 57.950, 281.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Maltose-binding periplasmic protein / MBP / MMBP / Maltodextrin-binding protein Mass: 40806.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody	synthetic Nanobody L2_G11 (a-MBP#2) Mass: 13876.341 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.17 Å³/Da / Density % sol: 43.32 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 100 mM Potassium thiocyanate, 30 % PEG2000MME

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00004 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 126132 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 16.98

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→49.307 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3

	R_factor	Num. reflection	% reflection
R_free	0.2156	6307	5 %
R_work	0.1904	-	-
obs	0.1917	126118	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→49.307 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7635	0	0	1040	8675

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7831
X-RAY DIFFRACTION	f_angle_d	0.591	10638
X-RAY DIFFRACTION	f_dihedral_angle_d	17.326	4629
X-RAY DIFFRACTION	f_chiral_restr	0.044	1143
X-RAY DIFFRACTION	f_plane_restr	0.004	1377

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 (%)
1.6-1.6182	0.3547	206	0.3157	3913	X-RAY DIFFRACTION	100
1.6182-1.6372	0.3249	207	0.3218	3923	X-RAY DIFFRACTION	100
1.6372-1.6572	0.3475	210	0.3043	3983	X-RAY DIFFRACTION	100
1.6572-1.6782	0.3557	205	0.2862	3901	X-RAY DIFFRACTION	100
1.6782-1.7002	0.2842	209	0.2838	3972	X-RAY DIFFRACTION	100
1.7002-1.7235	0.2957	206	0.2623	3908	X-RAY DIFFRACTION	100
1.7235-1.7482	0.2738	210	0.2641	3991	X-RAY DIFFRACTION	100
1.7482-1.7743	0.2883	206	0.2587	3919	X-RAY DIFFRACTION	100
1.7743-1.802	0.3179	208	0.2535	3957	X-RAY DIFFRACTION	100
1.802-1.8315	0.2649	207	0.244	3933	X-RAY DIFFRACTION	100
1.8315-1.8631	0.2676	211	0.231	4000	X-RAY DIFFRACTION	100
1.8631-1.897	0.2323	205	0.2261	3901	X-RAY DIFFRACTION	100
1.897-1.9335	0.233	213	0.2165	4049	X-RAY DIFFRACTION	100
1.9335-1.973	0.2231	206	0.2102	3899	X-RAY DIFFRACTION	100
1.973-2.0159	0.2464	208	0.2095	3957	X-RAY DIFFRACTION	100
2.0159-2.0627	0.2288	211	0.2057	4012	X-RAY DIFFRACTION	100
2.0627-2.1143	0.2716	208	0.2076	3944	X-RAY DIFFRACTION	100
2.1143-2.1715	0.2224	209	0.2026	3975	X-RAY DIFFRACTION	100
2.1715-2.2354	0.2076	211	0.1994	4019	X-RAY DIFFRACTION	100
2.2354-2.3075	0.2352	209	0.194	3973	X-RAY DIFFRACTION	100
2.3075-2.39	0.2231	209	0.1881	3967	X-RAY DIFFRACTION	100
2.39-2.4857	0.2215	212	0.187	4024	X-RAY DIFFRACTION	100
2.4857-2.5988	0.2182	209	0.1938	3973	X-RAY DIFFRACTION	100
2.5988-2.7358	0.2364	213	0.1903	4047	X-RAY DIFFRACTION	100
2.7358-2.9072	0.2235	213	0.187	4040	X-RAY DIFFRACTION	100
2.9072-3.1317	0.2173	210	0.1836	4001	X-RAY DIFFRACTION	100
3.1317-3.4467	0.1738	215	0.1704	4077	X-RAY DIFFRACTION	100
3.4467-3.9453	0.1942	214	0.161	4074	X-RAY DIFFRACTION	100
3.9453-4.9699	0.1646	218	0.1489	4135	X-RAY DIFFRACTION	100
4.9699-49.3305	0.1944	229	0.1809	4344	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	0.3444	-0.087	0.0852	0.073	-0.1477	0.2802	-0.15	0.1853	0.0148	-0.266	0.0707	-0.2702	0.0736	0.0278	-0	0.2694	-0.0246	0.0469	0.1917	-0.0083	0.2758	23.5282	37.4512	42.1818
2	0.4436	0.0027	0.2094	0.498	-0.2187	0.36	-0.0169	-0.2466	-0.1131	0.2763	0.0094	-0.1312	-0.0438	0.0621	-0	0.2892	0.0101	0.0081	0.2233	0.0026	0.2427	21.5058	33.8926	58.5793
3	0.4127	0.3149	-0.3523	1.0505	-0.632	0.4984	0.0742	-0.0526	0.0061	0.1834	-0.0367	0.1607	-0.019	-0.0327	0.0033	0.273	-0.0369	0.035	0.2184	-0.0011	0.2047	3.3085	13.3216	61.0504
4	0.7518	0.5423	-0.407	1.314	-0.644	0.3973	-0.0172	0.0132	-0.0107	0.0822	0.0378	0.0326	0.0571	-0.0765	-0.0021	0.2677	-0.0286	0.0289	0.1929	-0.0055	0.1691	7.1309	16.4677	54.6004
5	0.285	0.0486	0.0043	0.1271	-0.0195	0.0763	-0.1138	0.1012	0.186	-0.08	0.2211	0.39	-0.0118	-0.0613	0	0.2344	-0.0135	0.0352	0.207	0.0248	0.2938	6.0279	34.9768	46.6691
6	0.1201	0.213	-0.2137	0.2653	-0.3109	0.2817	-0.0905	0.0064	0.1203	0.1806	-0.005	0.0357	-0.0758	-0.0029	-0	0.2979	-0.0214	0.0326	0.2272	0.029	0.2847	5.4154	24.2981	59.0141
7	0.3324	-0.1893	0.0394	0.1292	0.0846	0.1553	0.0776	-0.1299	-0.273	0.2877	-0.3784	-0.6621	0.0984	0.3182	-0.0008	0.3731	-0.0242	-0.0673	0.3623	0.1317	0.4166	16.0897	5.9138	69.2665
8	0.088	0.0788	0.0373	0.4328	-0.0297	0.273	-0.0641	-0.1593	0.4729	0.0738	0.0586	-0.2117	-0.011	-0.059	0.0143	0.1635	-0.0158	0.0294	0.2427	-0.0457	0.3656	22.3138	40.2576	26.0557
9	0.5335	0.4367	0.1509	0.4193	-0.2791	0.6091	-0.0769	0.318	0.3019	-0.3651	0.0346	-0.1009	0.0693	0.081	-0.104	0.3018	-0.0161	0.0731	0.3418	0.0752	0.269	18.2418	36.04	10.2447
10	1.2763	0.6364	0.2969	1.5874	0.0833	0.4745	-0.0395	-0.0038	-0.0111	-0.204	0.009	-0.0472	0.1898	-0.0912	-0.0437	0.2459	-0.0758	0.0422	0.255	-0.0258	0.0296	2.9389	20.3827	14.8722
11	0.414	0.3532	-0.0028	0.4714	0.1872	0.1625	-0.0764	0.0637	0.0732	-0.3612	0.0868	0.0271	0.2027	-0.1417	0.0048	0.3495	-0.0883	-0.0719	0.36	0.0461	0.1406	-2.6517	25.8444	4.7283
12	0.0279	0.0031	0.0101	0.0013	0.0056	0.0074	-0.0371	-0.2937	0.0219	0.1922	0.0818	-0.2593	-0.1638	0.2935	0	0.3071	0.0047	-0.0043	0.3196	-0.0996	0.4598	36.182	13.4699	51.7348
13	0.0327	-0.0086	0.0018	0.0132	0.0072	0.0019	0.1776	0.3182	0.0733	-0.2269	-0.1041	-0.144	-0.1168	0.319	0.0001	0.2672	-0.0204	0.0649	0.4083	-0.0817	0.4078	35.6086	-0.5431	29.9451
14	-0.0066	0.0152	-0.0124	-0.0026	-0.0145	0.0287	-0.054	-0.0874	-0.1814	0.1892	0.0996	-0.1765	0.0138	0.1819	-0.0001	0.2365	0.0159	-0.0028	0.2972	-0.0595	0.3426	35.8763	3.9285	46.2141
15	0.1471	0.0356	-0.0385	0.1612	0.1097	0.0786	0.1319	-0.1397	0.1417	-0.0257	0.1273	-0.0903	-0.2218	0.11	-0.0001	0.289	0.0107	0.0493	0.2259	-0.0213	0.2864	27.359	8.959	50.5609
16	0.1735	-0.0027	0.0968	0.0507	0.0733	0.0979	-0.062	0.3631	-0.0806	0.1139	-0.2022	0.0942	-0.2994	0.0289	-0.0056	0.3093	0.0291	0.0943	0.2441	0.098	0.3832	23.81	10.8539	38.3912
17	0.0709	-0.0202	-0.0377	0.1231	0.0619	0.0823	0.0891	-0.0691	-0.2733	0.1939	-0.0139	0.1453	0.1741	-0.1175	0.0001	0.2631	-0.0061	0.0506	0.2346	0.0366	0.3346	22.2499	-0.399	44.6682
18	0.033	0.0301	0.0023	0.0578	-0.0174	0.0191	-0.2228	-0.0343	-0.1347	-0.0094	0.1629	-0.3628	0.1969	0.117	-0.0002	0.234	0.0599	-0.0208	0.2445	-0.0053	0.3601	33.3759	-0.2037	48.1214
19	-0.003	-0.0024	-0.0154	0.0153	0.0067	0.0436	0.1105	0.4366	-0.3393	-0.3037	0.1503	0.2835	-0.0354	-0.089	-0	0.3138	-0.0041	0.0167	0.3077	-0.0054	0.3505	27.7703	1.3376	29.6983
20	0.1813	-0.0185	0.1222	0.0426	0.0362	0.0826	-0.0335	-0.0628	0.3231	0.0076	0.1958	-0.1443	0.3058	-0.0509	-0	0.3046	0.0133	0.0332	0.2306	-0.0074	0.3411	23.4282	11.8187	47.3377
21	0.0443	0.0469	0.0341	0.0754	0.0439	0.1	-0.0986	-0.067	0.1248	-0.1369	0.1223	-0.1799	-0.1379	0.0315	-0	0.2924	0.0078	0.0525	0.2016	-0.0015	0.2776	26.4988	15.4134	47.5885
22	-0.0026	0.0049	0.0166	0.0166	0.0012	0.0437	0.3049	0.2017	0.2343	-0.4198	-0.1662	-0.0402	0.083	0.0612	-0.0001	0.4046	-0.0158	0.1018	0.3587	-0.0502	0.3238	34.4977	5.8742	29.8842
23	0.03	-0.0047	0.0445	0.0406	-0.0029	0.0355	0.0156	0.1241	0.3389	-0.2855	0.0763	0.0995	-0.4373	0.3805	0.0001	0.349	-0.0297	0.0613	0.4065	0.0452	0.7004	-1.757	-6.7007	14.7558
24	0.1271	-0.0294	0.0759	-0.0586	-0.0095	0.0497	0.078	-0.0168	0.4543	-0.0757	-0.2334	-0.0189	-0.2994	-0.0544	-0	0.253	0.0335	0.0752	0.2686	-0.0341	0.5588	-13.6642	-4.6986	27.1873
25	0.1083	0.0893	-0.0614	0.086	0.0068	0.0503	0.091	0.0718	0.3135	-0.0905	0.0969	0.0698	-0.0041	0.2646	0.0041	0.2033	0.0154	0.0285	0.3133	-0.0102	0.4083	-6.2477	-15.1864	17.2379
26	0.0378	-0.0281	-0.033	0.2958	-0.1621	0.1101	0.0088	-0.0681	0.0478	0.0413	0.2099	0.1608	0.1512	0.3394	0.029	0.1565	0.0313	-0.0105	0.373	-0.1386	0.4146	-4.2531	-16.4662	29.9082
27	0.1155	0.0628	-0.1031	0.0606	0.0093	0.0755	0.0512	0.1623	-0.0905	0.0465	-0.078	0.007	0.0195	-0.2957	0.0024	0.1797	0.0277	-0.0166	0.2929	-0.0555	0.4988	-15.5918	-19.1993	23.9027
28	0.0956	-0.1837	-0.072	0.411	0.2453	0.1965	0.2848	0.0303	0.5096	0.0207	-0.4405	0.0253	0.2059	0.0949	-0.0388	0.1673	0.1162	0.0026	0.2965	0.0002	0.5739	-14.9894	-9.6546	26.6722
29	0.0445	0.0323	-0.0536	0.4296	-0.9291	2.1325	0.195	-0.0306	0.7355	-0.3151	0.0872	-0.05	0.3747	-0.1653	0.149	0.0769	0.0232	0.0251	0.3137	-0.0964	0.4789	-3.3965	-18.5584	21.1008
30	0.0204	-0.1299	0.0882	0.0824	-0.246	0.7252	0.2517	-0.0446	0.5475	-0.1386	-0.0542	0.0735	-0.0175	0.119	0.062	0.1364	-0.0317	0.0567	0.2763	-0.0887	0.5194	-3.1669	-11.6751	25.6803

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 105 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 106 through 185 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 186 through 282 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 283 through 314 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 315 through 333 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 334 through 366 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 42 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 43 through 105 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 106 through 314 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 315 through 366 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid -1 through 7 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 8 through 17 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 18 through 26 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 27 through 39 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 40 through 52 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 53 through 73 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 74 through 83 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 84 through 91 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 92 through 108 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 109 through 118 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 119 through 125 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid -1 through 7 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 8 through 26 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 27 through 39 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 40 through 52 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 53 through 73 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 74 through 91 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 92 through 108 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 109 through 125 )

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