PDB-5m15: Synthetic nanobody in complex with MBP

ID or keywords:

Entry

Database: PDB / ID: 5m15

Title

Synthetic nanobody in complex with MBP

Components

Maltose-binding periplasmic protein
Synthetic nanobody L2_D09, (a-MBP#3)

Keywords

IMMUNE SYSTEM /

nanobody / synthetic library /

maltose binding protein

Function / homology

Function and homology information

detection of maltose stimulus /

maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / 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: 1.9 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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Download

PDBx/mmCIF format	5m15.cif.gz	396.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5m15.ent.gz	337.2 KB	Display	PDB format
PDBx/mmJSON format	5m15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m1/5m15 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m15	HTTPS FTP

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Related structure data

Related structure data	5m13C 5m14C C: citing same article (ref.)
Similar structure data	5m14-3 5m14-2 5fs7-1 4ksl-8 1efp-1 5mu3-2 5m14-1 2xbz-d 4ksl-6 4r8h-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

5m14C

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	#136 - Apr 2011 Nanobodies similarity (1) #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_D09, (a-MBP#3)

D: Synthetic nanobody L2_D09, (a-MBP#3)

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

1

D: Synthetic nanobody L2_D09, (a-MBP#3)

B: Maltose-binding periplasmic protein

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

2

A: Maltose-binding periplasmic protein

C: Synthetic nanobody L2_D09, (a-MBP#3)

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

3

B: Maltose-binding periplasmic protein

D: Synthetic nanobody L2_D09, (a-MBP#3)

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

Unit cell

Length a, b, c (Å)	57.030, 57.780, 286.530
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_D09, (a-MBP#3) Mass: 13841.399 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 / Water Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.16 Å³/Da / Density % sol: 43.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 100 mM Sodium acetate, 200 mM Ammonium acetate, 30 % PEG4000, pH 4.6

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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: Feb 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: 1.9→50 Å / Num. obs: 75931 / % possible obs: 100 % / Redundancy: 12.9 % / Net I/σ(I): 21.44

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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: 1.9→49.437 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.37

	R_factor	Num. reflection	% reflection
R_free	0.257	3797	5 %
R_work	0.2092	-	-
obs	0.2116	75931	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→49.437 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7619	0	0	422	8041

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7807
X-RAY DIFFRACTION	f_angle_d	0.623	10598
X-RAY DIFFRACTION	f_dihedral_angle_d	18.591	4621
X-RAY DIFFRACTION	f_chiral_restr	0.043	1137
X-RAY DIFFRACTION	f_plane_restr	0.004	1370

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 (%)
1.9-1.9241	0.3466	138	0.3315	2618	X-RAY DIFFRACTION	100
1.9241-1.9494	0.3892	138	0.3218	2623	X-RAY DIFFRACTION	100
1.9494-1.9761	0.3937	139	0.3214	2649	X-RAY DIFFRACTION	100
1.9761-2.0043	0.3509	138	0.312	2614	X-RAY DIFFRACTION	100
2.0043-2.0343	0.3323	139	0.291	2653	X-RAY DIFFRACTION	100
2.0343-2.0661	0.3384	138	0.2863	2612	X-RAY DIFFRACTION	100
2.0661-2.0999	0.3355	138	0.27	2627	X-RAY DIFFRACTION	100
2.0999-2.1361	0.3045	141	0.2625	2676	X-RAY DIFFRACTION	100
2.1361-2.175	0.3205	137	0.2669	2603	X-RAY DIFFRACTION	100
2.175-2.2168	0.2865	140	0.2567	2654	X-RAY DIFFRACTION	100
2.2168-2.2621	0.3198	139	0.2564	2638	X-RAY DIFFRACTION	100
2.2621-2.3113	0.3038	140	0.2562	2667	X-RAY DIFFRACTION	100
2.3113-2.365	0.3115	138	0.2466	2620	X-RAY DIFFRACTION	100
2.365-2.4242	0.2863	139	0.237	2651	X-RAY DIFFRACTION	100
2.4242-2.4897	0.2737	141	0.2308	2666	X-RAY DIFFRACTION	100
2.4897-2.563	0.3179	139	0.2347	2650	X-RAY DIFFRACTION	100
2.563-2.6457	0.2827	140	0.2293	2657	X-RAY DIFFRACTION	100
2.6457-2.7402	0.2813	141	0.2354	2680	X-RAY DIFFRACTION	100
2.7402-2.8499	0.2622	141	0.2282	2680	X-RAY DIFFRACTION	100
2.8499-2.9796	0.2701	140	0.2332	2657	X-RAY DIFFRACTION	100
2.9796-3.1367	0.2861	142	0.2218	2700	X-RAY DIFFRACTION	100
3.1367-3.3332	0.2775	141	0.2143	2668	X-RAY DIFFRACTION	100
3.3332-3.5905	0.218	142	0.1978	2713	X-RAY DIFFRACTION	100
3.5905-3.9516	0.2165	142	0.1796	2695	X-RAY DIFFRACTION	100
3.9516-4.5231	0.2288	145	0.1556	2759	X-RAY DIFFRACTION	100
4.5231-5.6973	0.2143	146	0.1612	2775	X-RAY DIFFRACTION	100
5.6973-49.4541	0.2042	155	0.1803	2929	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	0.3944	0.1458	-0.1875	0.2412	0.1383	0.3378	-0.0415	0.0068	-0.1971	-0.1256	-0.0081	-0.4482	0.0182	-0.0425	0.0038	0.3753	-0.0898	0.0261	0.2338	-0.051	0.4989	22.1178	32.5972	46.7509
2	0.0644	-0.0856	-0.0606	0.3327	-0.4526	0.4547	0.0628	-0.1711	-0.1576	0.2385	-0.0572	-0.2241	-0.1074	-0.2123	-0	0.4077	-0.1165	-0.0206	0.325	-0.0178	0.2069	10.4789	31.6309	59.7314
3	0.5758	-0.3012	0.4021	1.0464	-0.6033	0.1051	-0.1956	-0.7527	-0.1956	0.0557	0.7362	-0.0307	0.5671	-0.1763	0.7058	0.6286	-0.3084	-0.0059	0.4332	0.2073	0.1471	0.8961	7.0649	61.5452
4	0.7539	-0.1143	0.3779	1.1017	-0.8484	1.1939	0.01	-0.2108	0.0207	-0.0786	0.1337	-0.0867	0.14	-0.2622	0.0239	0.3538	-0.1195	0.0201	0.3071	-0.0434	0.1774	6.5343	20.4467	55.7045
5	0.1368	0.1884	-0.1259	0.48	-0.0483	0.1666	0.0874	-0.0417	0.1653	-0.0322	0.0216	0.0706	-0.0849	0.0307	0	0.272	-0.0608	0.0894	0.2498	-0.0497	0.3534	15.1265	40.4132	20.7957
6	0.098	-0.122	-0.062	0.084	0.0675	0.0318	0.1063	0.2271	0.0442	-0.2933	0.0522	-0.126	-0.0169	0.0975	0.0001	0.3084	-0.0363	0.054	0.3312	-0.0392	0.2949	18.3422	29.2197	7.0903
7	0.767	0.2452	-0.2683	0.4302	0.3769	0.8996	0.0587	0.0063	0.0085	0.0327	-0.0263	-0.0165	0.0611	-0.1627	0.0196	0.1837	-0.0448	0.0182	0.2472	-0.0219	0.2168	-0.5023	19.5618	14.6101
8	0.3637	-0.1693	-0.109	0.352	0.3602	0.3848	0.1964	0.5864	0.4206	-0.149	0.1958	0.2272	-0.4551	-0.4096	0.1536	0.3227	0.1042	-0.0065	0.6227	0.1579	0.425	-13.1681	28.9956	0.5203
9	0.0165	-0.0023	-0.0031	-0.0021	-0.0085	0.0248	-0.1162	-0.3304	-0.2137	0.3573	-0.1172	-0.1562	-0.1932	0.0971	-0	0.5795	-0.0629	-0.1134	0.6648	-0.1004	0.7016	32.9783	12.2442	50.913
10	0.1956	-0.0341	0.1493	0.0976	-0.0482	0.101	0.1704	-0.1633	0.0253	-0.1448	0.2165	-0.8163	-0.2636	0.0155	0.0001	0.4624	-0.1217	0.0477	0.4326	-0.0856	0.6603	28.0839	3.9997	44.1573
11	0.0936	-0.0051	0.08	-0.0077	-0.014	0.0517	-0.0322	0.5431	-0.0145	0.3357	-0.1965	-0.0069	0.0767	-0.1036	-0.0011	0.5437	0.0124	0.1706	0.4516	0.0515	0.527	19.848	9.1375	38.715
12	0.0198	-0.027	-0.0103	0.0059	-0.0098	0.0102	0.1489	-0.0481	-0.3834	0.2573	-0.2223	0.0259	0.1192	-0.1276	0	0.5915	-0.0449	0.0982	0.3832	0.1187	0.3888	17.0868	-1.409	51.1034
13	0.0613	-0.0185	-0.1257	0.0272	0.0088	0.2658	0.151	0.2391	-0.2892	0.1365	0.1066	-0.3474	-0.1047	-0.2465	0.0102	0.4154	-0.0881	0.0735	0.3174	-0.0167	0.422	20.6163	-2.1931	40.7019
14	0.1873	-0.022	-0.2316	0.0055	0.0275	0.3031	0.2236	0.0699	-0.0117	-0.1047	0.2919	-0.6953	-0.085	-0.2803	0.0217	0.5016	-0.0401	-0.019	0.2939	-0.0202	0.5962	27.3372	-0.8448	39.8598
15	0.0189	-0.0041	-0.0393	0.0885	-0.0225	0.0229	-0.0196	0.0259	-0.1403	0.444	-0.0576	-0.5786	-0.0651	-0.0854	0	0.5487	-0.0255	0.0261	0.3612	-0.0258	0.5251	19.9286	10.3637	46.8455
16	0.0224	-0.0157	0.0389	0.0156	-0.0279	0.0429	-0.1601	-0.1452	0.1557	-0.1043	-0.4119	0.3377	-0.0555	0.1639	-0.0001	0.5696	-0.044	-0.0659	0.4893	-0.0643	0.9217	23.4409	14.1002	47.1635
17	0.3888	-0.375	-0.0532	0.3762	0.0291	0.0731	0.0936	0.135	-0.0072	0.0654	-0.2243	-0.0415	-0.059	0.0632	0.0265	0.5637	-0.1427	0.2647	0.4831	0.0245	1.0202	30.3278	4.3693	29.3139
18	0.6739	0.4005	0.0825	0.2469	0.05	0.0123	0.5584	0.1986	1.1042	-0.1195	-0.2998	0.1934	-0.0057	0.1021	-0.0182	0.5132	0.2746	0.2565	0.4407	0.2691	0.8573	-12.3769	-8.1754	19.4216
19	0.0681	-0.0069	-0.027	0.0916	-0.0528	0.0835	0.3962	-0.0433	0.7712	-0.0207	0.1471	-0.4952	0.2141	0.0975	0.0157	0.3183	0.0083	0.0248	0.3877	-0.1615	0.6693	-7.1455	-15.6628	28.2101
20	0.0337	0.0052	-0.0321	1.1329	0.2009	0.0475	0.058	0.498	0.2944	0.3958	0.029	-0.283	0.3142	-0.017	0.0335	0.2141	-0.0033	0.015	0.4412	-0.0436	0.4028	-16.0194	-21.2774	24.0446
21	1.0484	0.566	0.1842	0.8745	0.3524	0.1497	0.3533	0.244	0.5576	-0.1005	-0.3982	-0.1613	0.0198	0.0654	0.0545	0.3773	0.3162	0.2018	0.578	0.1759	0.4652	-19.0467	-11.2917	18.9587
22	0.4501	-0.3009	-0.0573	0.2943	0.1788	0.1568	0.4539	0.1148	0.9482	0.1533	-0.0662	-0.5923	0.1847	-0.1779	0.0107	0.4275	-0.0532	0.1239	0.4243	-0.135	0.8975	-12.5938	-11.731	31.0782
23	0.0023	-0.0155	0.0133	0.0122	-0.0181	0.0596	0.1176	0.2625	-0.1118	-0.0427	0.5042	-0.0594	-0.0397	-0.1845	0.0011	0.2921	-0.0108	0.0296	0.326	-0.0441	0.4408	-6.1198	-25.2285	17.8945
24	0.0333	0.012	-0.0186	0.0056	-0.0226	0.0171	0.1499	-0.1206	0.1646	-0.1126	0.0078	0.0784	0.1715	0.2599	0.0001	0.3543	0.0529	0.0675	0.5071	-0.0299	0.7363	-3.0665	-16.0006	20.1705
25	0.0244	0.0254	0.0038	0.0532	-0.0036	0.0024	0.1126	-0.0481	0.117	0.0979	-0.0232	-0.0309	0.0455	-0.0019	0.0889	0.375	-0.0776	0.1974	0.2793	-0.4566	1.1595	-12.5355	-4.9601	35.7448

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 72 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 73 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 218 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 219 through 366 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 72 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 73 through 105 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 106 through 333 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 334 through 367 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -1 through 7 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 8 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 52 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 53 through 60 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 61 through 73 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 74 through 91 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 92 through 108 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 109 through 118 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 119 through 125 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1 through 32 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 33 through 44 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 45 through 67 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 68 through 83 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 84 through 99 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 100 through 108 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 109 through 118 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 119 through 125 )

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi