PDB-5ovw: Nanobody-bound BtuF, the vitamin B12 binding protein in Escherich...

ID or keywords:

Entry

Database: PDB / ID: 5ovw

Title

Nanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli

Components

NanobodySingle-domain antibody
Vitamin B12-binding protein

Keywords

TRANSPORT PROTEIN /

Nanobody / Inhibitor /

vitamin B12 / substrate-binding protein

Function / homology

Function and homology information

cobalamin transport complex / cobalamin transport /

cobalamin binding / outer membrane-bounded periplasmic space /

periplasmic space /

membrane
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.653 Å

Authors

Mireku, S.A. / Sauer, M.M. / Glockshuber, R. / Locher, K.P.

Funding support

Switzerland, 1items

Citation

Journal: Sci Rep / Year: 2017
Title: Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD.
Authors: Mireku, S.A. / Sauer, M.M. / Glockshuber, R. / Locher, K.P.

History

Deposition	Aug 30, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ovw.cif.gz	876.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ovw.ent.gz	753.6 KB	Display	PDB format
PDBx/mmJSON format	5ovw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	4wem-d 4rtk-d 2bvn-2 3gge-d 6flk-d 2oen-d 3l3f-d 4wen-d 5ljw-1 6r9h-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) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Vitamin B12-binding protein

B: Vitamin B12-binding protein

C: Vitamin B12-binding protein

D: Vitamin B12-binding protein

E: Vitamin B12-binding protein

F: Vitamin B12-binding protein

G: Nanobody

H: Nanobody

I: Nanobody

J: Nanobody

K: Nanobody

L: Nanobody

hetero molecules

291 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Vitamin B12-binding protein

H: Nanobody

hetero molecules

defined by author&software
Evidence: gel filtration
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Vitamin B12-binding protein

I: Nanobody

hetero molecules

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

3

C: Vitamin B12-binding protein

G: Nanobody

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

4

D: Vitamin B12-binding protein

J: Nanobody

hetero molecules

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

5

E: Vitamin B12-binding protein

K: Nanobody

hetero molecules

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

6

F: Vitamin B12-binding protein

L: Nanobody

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.800, 141.000, 216.700
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Vitamin B12-binding protein Mass: 31511.924 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: OmpA-BtuF-3C-His6 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuF, yadT, b0158, JW0154 / Production host: Escherichia coli (E. coli) / References: UniProt: P37028
#2: Antibody	Nanobody / Single-domain antibody Mass: 16964.984 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: SecretionSignal-Nanobody-His6 / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.11 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Tris-HCl, Magnesium chloride

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99984 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99984 Å / Relative weight: 1
Reflection	Resolution: 2.653→19.996 Å / Num. obs: 63910 / % possible obs: 85.33 % / Redundancy: 6.8 % / Net I/σ(I): 1.36

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
Coot		model building
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.653→19.996 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2594	3239	5.07 %
R_work	0.2232	-	-
obs	0.2251	63910	85.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.653→19.996 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17058	0	30	264	17352

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	17479
X-RAY DIFFRACTION	f_angle_d	0.558	23797
X-RAY DIFFRACTION	f_dihedral_angle_d	12.987	10594
X-RAY DIFFRACTION	f_chiral_restr	0.043	2622
X-RAY DIFFRACTION	f_plane_restr	0.004	3126

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 (%)
2.6533-2.6928	0.5054	8	0.382	174	X-RAY DIFFRACTION	6
2.6928-2.7348	0.3261	29	0.3829	508	X-RAY DIFFRACTION	17
2.7348-2.7795	0.4048	48	0.3627	927	X-RAY DIFFRACTION	30
2.7795-2.8273	0.3387	101	0.3482	1534	X-RAY DIFFRACTION	51
2.8273-2.8786	0.4276	128	0.341	2176	X-RAY DIFFRACTION	71
2.8786-2.9338	0.3548	133	0.3401	2632	X-RAY DIFFRACTION	87
2.9338-2.9935	0.3513	152	0.3323	3030	X-RAY DIFFRACTION	98
2.9935-3.0583	0.3356	172	0.3352	3026	X-RAY DIFFRACTION	100
3.0583-3.1292	0.3453	175	0.3217	3059	X-RAY DIFFRACTION	100
3.1292-3.2071	0.3421	142	0.2995	3085	X-RAY DIFFRACTION	100
3.2071-3.2935	0.2949	150	0.2995	3066	X-RAY DIFFRACTION	100
3.2935-3.39	0.3451	146	0.2902	3101	X-RAY DIFFRACTION	100
3.39-3.4988	0.2958	150	0.2663	3115	X-RAY DIFFRACTION	100
3.4988-3.6232	0.2859	158	0.2452	3076	X-RAY DIFFRACTION	100
3.6232-3.7673	0.3085	174	0.2445	3051	X-RAY DIFFRACTION	100
3.7673-3.9375	0.2858	180	0.217	3074	X-RAY DIFFRACTION	100
3.9375-4.1434	0.2284	161	0.1917	3097	X-RAY DIFFRACTION	100
4.1434-4.4004	0.212	167	0.1727	3124	X-RAY DIFFRACTION	100
4.4004-4.736	0.2175	166	0.1631	3091	X-RAY DIFFRACTION	100
4.736-5.2049	0.2015	175	0.1621	3118	X-RAY DIFFRACTION	100
5.2049-5.9408	0.2113	170	0.1722	3146	X-RAY DIFFRACTION	100
5.9408-7.4206	0.2137	163	0.1822	3190	X-RAY DIFFRACTION	100
7.4206-19.9969	0.1698	191	0.1504	3271	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	0.1708	0.0853	0.0757	0.1471	0.0004	0.2454	0.0865	-0.0653	0.0345	0.1699	0.0902	0.2041	-0.0247	-0.1083	0.0722	0.4355	0.0053	0.0899	0.3995	-0.0202	0.5218	4.9604	153.3823	6.6091
2	0.107	-0.1471	-0.0377	0.1897	-0.0242	0.056	0.0835	0.035	0.1166	0.1325	-0.0554	-0.0891	0.0285	-0.0544	0	0.3814	-0.055	-0.034	0.4025	-0.0494	0.5142	31.5942	149.7825	5.6018
3	0.6538	0.1149	0.0221	0.2796	0.1127	0.5772	-0.3603	0.1352	0.2691	-0.1953	0.1396	0.2694	-0.3722	0.0086	-0.4169	0.6229	-0.0854	-0.1566	0.4489	0.0297	0.4551	2.0563	122.2943	-29.013
4	0.1208	0.0284	0.0413	0.7057	-0.1114	0.0564	-0.0549	0.2092	-0.2876	-0.0108	0.3391	0.0454	0.1265	0.44	0.4794	0.3183	0.1657	-0.0118	0.6449	-0.1868	0.399	11.901	97.2695	-27.5641
5	0.1713	-0.0867	0.0773	0.2303	0.2224	0.202	0.1489	-0.1522	0.0918	0.1574	-0.0153	0.2037	0.0062	-0.0564	0.2676	0.5495	-0.0305	0.1909	0.486	-0.1355	0.5135	4.9192	157.3757	28.3533
6	0.0359	0.0277	0.0077	0.1212	0.1012	0.0783	0.151	0.157	0.5511	0.0294	0.1346	-0.1939	-0.2922	0.1191	0.023	0.7671	-0.2599	0.353	0.8188	-0.1061	0.9438	16.2098	181.8245	26.5416
7	0.1625	0.0722	0.2204	0.1579	-0.0334	0.2503	0.0007	-0.1455	0.2562	0.0161	-0.1275	0.2706	-0.1105	-0.0711	-0.1836	0.3676	0.0103	-0.0635	0.4194	-0.1151	0.5075	3.5659	125.9294	-7.2848
8	0.1249	0.152	0.0786	0.221	0.0439	0.0756	-0.075	-0.0209	0.1508	-0.1196	0.0603	-0.0424	-0.1461	0.0437	-0.0007	0.2941	-0.0403	0.0372	0.3676	-0.0608	0.4203	30.4807	127.8683	-7.731
9	0.1284	0.2671	0.1324	0.5015	0.2119	0.3321	-0.052	0.096	-0.2058	0.172	0.1824	-0.0116	0.2841	-0.1154	0.242	0.3834	-0.0474	0.0934	0.4828	0.0532	0.316	21.0245	101.4999	43.9537
10	0.2373	-0.1218	0.0239	0.2622	-0.1478	0.1497	-0.2302	-0.2488	0.0513	0.4993	0.2994	-0.1043	-0.1756	0.0837	0.1223	0.6319	0.0294	-0.0659	0.4191	-0.1202	0.3746	35.3883	124.4239	42.2568
11	0.4402	0.3465	-0.123	0.5181	0.2868	0.3893	0.216	0.2994	0.0553	0.3092	0.0087	-0.0616	0.2315	-0.1231	0.0847	0.7213	-0.0784	0.1109	0.4168	0.0206	0.4151	18.3527	102.2896	65.7283
12	0.0061	0.0093	0.0282	0.0375	0.0397	0.0821	-0.4588	0.0692	0.2084	-0.294	0.072	0.541	0.1755	-0.1697	-0.1567	0.8586	0.0905	-0.0114	0.5602	0.2455	0.9429	0.0944	122.0881	65.1581
13	0.2391	-0.1479	-0.0615	0.1048	-0.0027	0.0508	0.2941	-0.0205	0.1734	0.4209	-0.3484	-0.4244	-0.0861	0.1503	-0.0074	0.824	-0.2305	-0.1038	0.9643	-0.3329	0.9027	31.75	160.5457	41.9097
14	0.1055	0.137	0.0156	0.2177	-0.1079	0.1301	-0.1189	0.0443	0.0748	-0.1751	0.2037	-0.1667	0.0074	-0.1229	0.0848	0.5429	-0.0939	0.0625	0.2864	0.0039	0.44	19.7757	172.9447	-10.9603
15	0.419	-0.2024	-0.5111	0.1453	0.1308	0.6675	-0.3176	0.5249	0.0552	0.0189	-0.2754	-0.065	-0.0648	0.7385	-1.0911	0.3069	-0.5219	0.3768	2.0021	-0.0655	-0.07	27.7344	118.0333	-43.8302
16	0.0899	-0.018	-0.0328	0.2683	0.3187	0.3848	0.1422	-0.0556	-0.2093	-0.073	0.0095	-0.0613	0.0327	-0.0185	0.2316	0.2471	-0.0323	-0.0535	0.4121	-0.0122	0.3899	18.0617	105.2768	8.9181
17	0.0675	-0.1175	-0.0411	0.3313	0.1124	0.0319	-0.1497	-0.1916	-0.1556	0.3399	0.2871	0.2818	-0.0755	-0.3803	0.1609	0.3886	0.0849	0.1201	0.6759	0.1481	0.4403	8.38	123.3896	27.8456
18	0.0485	0.0952	0.1028	0.0894	0.0826	0.1191	-0.0643	-0.0058	0.1127	-0.2036	0.1352	0.0883	-0.055	0.1046	0.1054	0.8211	-0.283	0.1984	0.4981	-0.168	0.6444	26.4387	127.5614	79.6433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 149 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 266 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 22 through 149 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 150 through 266 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 22 through 149 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 150 through 266 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 22 through 149 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 150 through 266 )
9	X-RAY DIFFRACTION	9	chain 'E' and (resid 22 through 149 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 150 through 266 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 22 through 149 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 150 through 266 )
13	X-RAY DIFFRACTION	13	chain 'G' and (resid 24 through 149 )
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 24 through 149 )
15	X-RAY DIFFRACTION	15	chain 'I' and (resid 24 through 149 )
16	X-RAY DIFFRACTION	16	chain 'J' and (resid 24 through 149 )
17	X-RAY DIFFRACTION	17	chain 'K' and (resid 24 through 149 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 24 through 149 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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