PDB-5m13: Synthetic nanobody in complex with MBP

ID or keywords:

Entry

Database: PDB / ID: 5m13

Title

Synthetic nanobody in complex with MBP

Components

Maltose-binding periplasmic protein
synthetic Nanobody L2_C06 (a-MBP#2)

Keywords

IMMUNE SYSTEM / nanobody / synthetic library / maltose binding protein

Function / homology

Function and homology information

detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / 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 (E. coli)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.372 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
Revision 1.3	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	5m13.cif.gz	220 KB	Display	PDBx/mmCIF format
PDB format	pdb5m13.ent.gz	172.6 KB	Display	PDB format
PDBx/mmJSON format	5m13.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5m13_validation.pdf.gz	439.7 KB	Display	wwPDB validaton report
Full document	5m13_full_validation.pdf.gz	441.1 KB	Display
Data in XML	5m13_validation.xml.gz	26.2 KB	Display
Data in CIF	5m13_validation.cif.gz	40.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m1/5m13 ftp://data.pdbj.org/pub/pdb/validation_reports/m1/5m13	HTTPS FTP

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Related structure data

Related structure data	5m14C 5m15C C: citing same article (ref.)
Similar structure data	1e32-d 4xm8-d 5zi1-2 1zk7-d 4k7z-d 1bui-d 4nik-d 6ovb-d 4arx-1 5k9h-d 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	#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: synthetic Nanobody L2_C06 (a-MBP#2)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	58.298, 82.789, 102.583
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.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: malE, b4034, JW3994 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9
#2: Antibody	synthetic Nanobody L2_C06 (a-MBP#2) Mass: 13785.271 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.75 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris pH 8.5, 25 % PEG3350

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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: 1.372→50 Å / Num. obs: 196280 / % possible obs: 97.79 % / Redundancy: 2.9 % / Net I/σ(I): 10.04

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Processing

Software

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

Refinement

Resolution: 1.372→47.666 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 18.23

	R_factor	Num. reflection	% reflection
R_free	0.186	9807	5 %
R_work	0.1682	-	-
obs	0.1691	196280	97.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.372→47.666 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3811	0	28	694	4533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3967
X-RAY DIFFRACTION	f_angle_d	0.75	5385
X-RAY DIFFRACTION	f_dihedral_angle_d	21.715	1450
X-RAY DIFFRACTION	f_chiral_restr	0.073	579
X-RAY DIFFRACTION	f_plane_restr	0.005	696

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 (%)
1.3721-1.3877	0.3261	211	0.2903	3970	X-RAY DIFFRACTION	62
1.3877-1.404	0.2931	322	0.275	6171	X-RAY DIFFRACTION	98
1.404-1.4211	0.3044	325	0.2602	6224	X-RAY DIFFRACTION	97
1.4211-1.4391	0.287	334	0.2543	6235	X-RAY DIFFRACTION	99
1.4391-1.4581	0.2525	326	0.2308	6207	X-RAY DIFFRACTION	97
1.4581-1.478	0.22	331	0.2238	6261	X-RAY DIFFRACTION	99
1.478-1.4992	0.2164	320	0.2174	6229	X-RAY DIFFRACTION	98
1.4992-1.5215	0.2313	331	0.2107	6323	X-RAY DIFFRACTION	100
1.5215-1.5453	0.2364	338	0.2093	6348	X-RAY DIFFRACTION	100
1.5453-1.5707	0.225	334	0.1943	6335	X-RAY DIFFRACTION	99
1.5707-1.5977	0.2277	330	0.189	6343	X-RAY DIFFRACTION	100
1.5977-1.6268	0.191	333	0.1891	6366	X-RAY DIFFRACTION	100
1.6268-1.6581	0.2262	336	0.1817	6374	X-RAY DIFFRACTION	100
1.6581-1.6919	0.1869	333	0.1755	6302	X-RAY DIFFRACTION	100
1.6919-1.7287	0.1881	332	0.1771	6308	X-RAY DIFFRACTION	100
1.7287-1.7689	0.215	337	0.1709	6382	X-RAY DIFFRACTION	100
1.7689-1.8132	0.1945	326	0.1789	6263	X-RAY DIFFRACTION	99
1.8132-1.8622	0.2121	332	0.1732	6283	X-RAY DIFFRACTION	99
1.8622-1.917	0.1991	335	0.1725	6333	X-RAY DIFFRACTION	99
1.917-1.9789	0.1933	330	0.1717	6344	X-RAY DIFFRACTION	100
1.9789-2.0496	0.1917	334	0.1632	6330	X-RAY DIFFRACTION	100
2.0496-2.1317	0.1991	337	0.1652	6294	X-RAY DIFFRACTION	99
2.1317-2.2287	0.1661	336	0.1571	6360	X-RAY DIFFRACTION	100
2.2287-2.3462	0.1903	332	0.1631	6345	X-RAY DIFFRACTION	100
2.3462-2.4932	0.1701	331	0.1576	6320	X-RAY DIFFRACTION	100
2.4932-2.6857	0.1794	335	0.1582	6284	X-RAY DIFFRACTION	99
2.6857-2.9559	0.1753	332	0.1655	6290	X-RAY DIFFRACTION	99
2.9559-3.3835	0.1677	326	0.1538	6039	X-RAY DIFFRACTION	95
3.3835-4.2625	0.1502	317	0.1438	6250	X-RAY DIFFRACTION	98
4.2625-47.6947	0.1553	331	0.1488	6360	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	0.1349	0.0932	0.0843	0.0495	-0.0092	0.2456	-0.0166	0.2169	-0.0322	-0.0566	0.0288	-0.0105	0.0465	-0.0241	-0.002	0.0972	0.001	-0.0042	0.1328	0.019	0.1217	-5.5055	-1.4454	-29.666
2	0.8865	-0.0316	0.2962	0.0481	-0.2099	0.4093	-0.0546	-0.0781	0.0764	0.0344	0.0242	-0.0134	-0.0629	-0.079	-0.1452	0.1142	0.0165	0.0026	0.0655	0.003	0.0998	2.5995	3.5229	-13.7402
3	0.9829	0.3982	-0.3406	0.235	-0.2541	0.4202	0.0537	-0.1079	0.0189	-0.0281	-0.0448	-0.0417	-0.0609	0.0702	0.0124	0.118	0.0242	0.0057	0.1053	0.0103	0.0993	23.8826	-0.2507	-2.7954
4	1.0252	0.0176	0.1775	0.0611	-0.068	0.3155	-0.0069	-0.0788	-0.0079	-0.0265	0.0148	0.0127	-0.0009	-0.0317	0.0189	0.1082	0.0128	0.0107	0.061	0.004	0.0897	10.0417	-1.8276	-10.5297
5	0.0923	0.1232	0.0317	0.1256	0.0657	0.0602	-0.061	0.2208	-0.105	0.0794	0.0147	0.0071	0.026	-0.0743	-0.023	0.1571	0.0204	-0.0027	0.2051	-0.0451	0.1258	3.2285	-6.9516	12.2959
6	-0.0217	-0.0246	0.0076	0.0083	0.0057	0.0197	-0.0626	0.2738	-0.189	0.0986	0.0326	0.0155	0.0848	-0.1275	0.0018	0.155	-0.0055	-0.0207	0.1714	-0.0514	0.1494	0.8941	-10.1802	15.6457
7	0.1812	-0.0102	-0.0833	0.0555	0.0482	0.2078	0.0493	0.1603	-0.0794	0.0926	0.0168	-0.0137	0.0398	-0.1012	0.0228	0.1321	-0.0215	-0.0197	0.1138	-0.0289	0.1124	5.9809	-7.1653	25.0349
8	0.0761	0.0043	0.0452	0.0841	0.1201	0.1234	0.029	-0.0309	-0.0105	0.0582	0.0316	0.0191	-0.0435	0.0291	0.0363	0.1149	-0.0096	0.008	0.1624	-0.0252	0.0959	7.6682	3.2138	19.4047
9	0.1129	-0.0394	-0.0219	0.0413	-0.0235	-0.0117	0.0358	-0.1376	-0.0627	0.2048	0.0392	0.0498	-0.2342	-0.2111	0	0.138	-0.0178	0.0013	0.1849	-0.0019	0.1104	-3.1619	2.6707	25.3883
10	0.2125	-0.0731	-0.1474	0.0244	0.0287	0.0712	0.001	0.4479	-0.1432	-0.078	-0.0841	-0.0765	0.1227	-0.3199	-0.0086	0.1315	-0.0338	0.0173	0.1486	-0.0717	0.157	-3.6529	-8.0532	19.424
11	0.0197	-0.019	-0.0047	0.0068	0.0006	-0.0005	0.0868	0.1265	0.168	0.0577	-0.0489	0.1319	-0.1783	-0.1514	0	0.1379	0.0424	0.0121	0.2364	0.014	0.1388	-2.3112	7.2938	9.945
12	0.1515	-0.0251	-0.0765	0.0483	0.0436	0.0358	0.0496	0.1101	0.0138	0.0351	-0.0497	-0.0314	0.0594	-0.0264	0.0003	0.1314	-0.0082	0.0024	0.1293	-0.0177	0.105	8.5242	-1.7214	24.772
13	0.2348	0.023	-0.0482	0.0427	-0.0465	0.093	0.0165	0.1497	-0.0134	-0.0278	-0.0767	-0.0868	0.0068	-0.0078	0.0056	0.1173	0.0098	-0.0053	0.1411	-0.0117	0.1082	9.0149	-1.9461	16.9828

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 128 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 129 through 218 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 219 through 366 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 0 through 17 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 26 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 39 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 52 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 53 through 67 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 68 through 83 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 84 through 91 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 92 through 108 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 109 through 125 )

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