PDB-4i13: Nanobody ca1697 binding to the DHFR.folate binary complex

ID or keywords:

Entry

Database: PDB / ID: 4i13

Title

Nanobody ca1697 binding to the DHFR.folate binary complex

Components

Dihydrofolate reductase
Protein ca1697 (nanobody)

Keywords

OXIDOREDUCTASE/IMMUNE SYSTEM / alpha/beta fold / immunoglobulin fold /

reductase /

NADPH / folate derivatives / reduction / OXIDOREDUCTASE-IMMUNE SYSTEM complex

Function / homology

Function and homology information

methotrexate binding /

dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process /

NADP+ binding /

folic acid binding / folic acid metabolic process / glycine biosynthetic process /

dihydrofolate reductase /

dihydrofolate reductase activity ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Oyen, D. / Steyaert, J. / Barlow, J.N.

Citation

Journal: To be Published
Title: Exploring an alternative antibody interaction mechanism
Authors: Oyen, D. / Steyaert, J. / Barlow, J.N.

History

Deposition	Nov 19, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 27, 2013	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4i13.cif.gz	133.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4i13.ent.gz	111.2 KB	Display	PDB format
PDBx/mmJSON format	4i13.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/4i13 ftp://data.pdbj.org/pub/pdb/validation_reports/i1/4i13	HTTPS FTP

-
Related structure data

Related structure data	4i1nC C: citing same article (ref.)
Similar structure data	4i1n-d 3n3w-d 5z8l-d 1lxa-d 5ees-d 3ewi-d 3hy8-d 7nbi-d 4l4w-1 4eze-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (10) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Dihydrofolate reductase

B: Protein ca1697 (nanobody)

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	49.760, 58.050, 114.380
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Dihydrofolate reductase / Mass: 18019.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Antibody	Protein ca1697 (nanobody) Mass: 14826.606 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-FOL / FOLIC ACID / Folate Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₉N₇O₆
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.51 Å³/Da / Density % sol: 51.09 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 17% w/v PEG 1500, 10% v/v MPD, 50mM PIPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2009
Radiation	Monochromator: Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8726 Å / Relative weight: 1
Reflection	Resolution: 1.6→20 Å / Num. all: 44517 / Num. obs: 44517 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / B_iso Wilson estimate: 13.12 Å²
Reflection shell	Resolution: 1.6→1.69 Å / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→19.611 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9075 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 15.51 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1803	2238	5.04 %
R_work	0.1542	-	-
obs	0.1554	44447	99.93 %
all	-	44517	-

Solvent computation

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

Displacement parameters

B_iso max: 58.33 Å² / B_iso mean: 18.3029 Å² / B_iso min: 4.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.9445 Å²	-0 Å²	0 Å²
2-	-	-1.0769 Å²	-0 Å²
3-	-	-	0.1324 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→19.611 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2240	0	32	384	2656

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2384
X-RAY DIFFRACTION	f_angle_d	1.051	3252
X-RAY DIFFRACTION	f_dihedral_angle_d	15.138	875
X-RAY DIFFRACTION	f_chiral_restr	0.074	350
X-RAY DIFFRACTION	f_plane_restr	0.005	423

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6348	0.1985	155	0.1689	2537	2692	100
1.6348-1.6728	0.1867	159	0.1612	2599	2758	100
1.6728-1.7146	0.184	123	0.1515	2620	2743	100
1.7146-1.7609	0.1851	138	0.1523	2594	2732	100
1.7609-1.8127	0.1807	138	0.1527	2626	2764	100
1.8127-1.8712	0.181	143	0.1499	2595	2738	100
1.8712-1.938	0.1705	131	0.1456	2619	2750	100
1.938-2.0155	0.1554	144	0.1493	2604	2748	100
2.0155-2.1071	0.1522	136	0.1428	2628	2764	100
2.1071-2.2181	0.1854	142	0.1514	2625	2767	100
2.2181-2.3568	0.1878	144	0.1614	2637	2781	100
2.3568-2.5385	0.19	137	0.1683	2657	2794	100
2.5385-2.7933	0.2124	118	0.162	2669	2787	100
2.7933-3.196	0.1759	136	0.1604	2687	2823	100
3.196-4.0209	0.1698	139	0.1447	2708	2847	100
4.0209-19.6125	0.1831	155	0.1534	2804	2959	99

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	4.7912	0.3102	-1.7597	1.0673	-0.2478	3.0561	-0.1303	-0.2298	-0.6719	0.0547	-0.2268	-0.6703	0.2254	0.3344	0.0329	0.0371	0.0071	-0.0091	0.0947	0.0712	0.196	48.9907	47.1003	19.3508
2	0.124	-0.1095	-0.1634	2.803	0.5696	0.261	-0.0591	-0.0429	-0.1884	-0.2695	-0.0036	-0.043	0.0008	0.0635	0.0318	0.1109	0.0034	-0.0185	0.0847	0.0391	0.1739	51.834	58.0456	12.2606
3	6.8758	-0.1466	-3.2254	3.1105	-1.924	6.0002	-0.2141	0.1829	-0.122	-0.5257	0.0638	0.0228	0.0249	-0.1852	0.084	0.1169	-0.0177	-0.014	0.0762	0.0119	0.0698	41.5358	48.5937	8.3656
4	1.8531	-0.091	-0.1634	1.6195	-0.1724	1.1671	0.044	0.0774	0.0814	0.0526	0.0521	0.1138	-0.0414	-0.1519	-0.0688	0.0628	-0.0001	-0.0026	0.0981	0.0233	0.0593	36.0412	57.3515	18.0781
5	2.0973	0.8616	2.0847	2.7898	-1.124	7.7162	-0.1614	-0.3999	0.4674	0.2854	0.1309	0.1263	-0.5574	-0.3231	-0.0034	0.1698	0.0557	0.0211	0.1778	-0.0272	0.1202	32.781	65.0763	25.1452
6	1.5499	-0.2845	0.7832	2.9346	-1.1338	2.535	-0.0806	-0.2568	-0.2006	0.4391	0.1147	0.1884	-0.0053	-0.1442	0.0188	0.1473	0.0148	0.0334	0.1743	0.0453	0.0866	32.593	54.3408	29.7607
7	2.2365	-0.4473	-0.6115	2.656	-0.0522	2.6959	-0.0764	-0.2453	-0.0798	0.224	0.0043	-0.2436	0.1326	0.2001	0.0236	0.0976	0.0025	-0.0329	0.0834	0.0328	0.103	46.6907	47.6718	21.8143
8	1.3941	0.0399	-1.2669	0.9568	0.3127	3.6148	-0.0773	-0.1782	-0.1533	-0.2628	-0.0365	-0.4156	0.5947	0.3626	0.0501	0.2534	0.0122	0.0502	0.1076	0.0262	0.1906	50.644	36.9875	14.9464
9	1.585	0.9349	-0.9853	2.5559	-1.4746	3.2534	-0.2057	0.0018	-0.2214	-0.3729	-0.0591	-0.5418	0.242	0.0631	0.198	0.2134	0.0064	0.0623	0.09	0.0235	0.1756	50.907	44.1818	9.1221
10	1.3778	-0.0524	-0.7406	1.8885	-0.9299	5.292	-0.0861	-0.0465	0.1337	0.3196	-0.0793	-0.0301	-0.2673	0.153	0.1756	0.1225	-0.0082	-0.0169	0.0793	0.0203	0.1392	50.6772	85.7324	2.5825
11	1.7037	0.2694	-0.9066	1.4389	-0.5331	8.2733	-0.1939	-0.1301	0.1808	0.238	-0.0389	-0.1116	0.0265	0.1559	0.2192	0.1136	0.0084	-0.0196	0.1018	0.0227	0.1144	54.2658	81.9664	4.1893
12	3.1641	2.5664	0.6213	8.9032	1.1266	0.1808	-0.0007	-0.5014	0.1241	0.6465	-0.0481	-0.0679	-0.2883	-0.0421	0.093	0.2317	0.0126	-0.0412	0.1518	-0.003	0.103	53.63	72.777	18.301
13	2.5066	-1.0443	2.5931	2.3432	-2.4075	3.7984	-0.0809	0.0899	0.1577	0.1695	0.0257	0.0559	-0.1975	-0.0576	0.01	0.0604	0.0135	0.0115	0.0417	0.0218	0.0578	44.2105	77.7839	4.6247
14	1.744	-1.062	0.036	1.6514	0.0741	0.1897	-0.0254	0.156	0.3712	-0.1074	-0.0017	0.0592	0.031	-0.06	0.0464	0.0317	-0.0069	-0.0169	0.0752	0.0508	0.1419	40.1345	77.0597	1.8029
15	0.9885	0.0571	1.5807	0.7543	0.0744	3.6958	0.0558	0.1054	-0.0488	0.0452	0.01	-0.0704	0.1642	0.1872	-0.099	0.0546	0.0082	-0.009	0.0552	0.0072	0.0796	51.8654	67.5723	5.5496
16	2.6416	-1.3985	0.4504	1.4539	-1.4523	3.7742	0.1282	0.2663	-0.1257	-0.1262	0.0137	0.0895	0.1962	0.1164	-0.1562	0.076	-0.0111	-0.0058	0.0656	0.0089	0.0933	50.2066	72.6154	-2.1669
17	2.4727	-0.2748	1.4982	1.7865	-0.9011	4.399	0.1089	-0.133	0.1736	0.3053	0.1365	-0.1287	-0.3996	0.2718	-0.1358	0.1259	0.0025	-0.0109	0.1379	-0.0101	0.1003	56.7214	77.4934	5.9206
18	1.1985	-0.4071	-0.5547	1.5788	-1.5406	2.9997	0.0496	0.1428	-0.0014	0.0657	0.0665	0.0416	-0.1369	-0.168	-0.1281	0.0652	-0.0124	-0.0059	0.0841	0.0187	0.1046	44.8371	81.0828	-2.1422
19	3.8345	-0.3787	0.1667	3.105	-0.0023	3.4443	0.0538	-0.1239	-0.1372	0.0323	0.1072	0.2835	0.0384	-0.214	-0.1313	0.0666	-0.0119	0.0035	0.0762	0.0398	0.1013	40.579	68.813	9.5583
20	4.5339	1.3432	1.1929	6.9933	0.6232	3.7293	0.1171	-0.5569	-0.022	0.5062	-0.1312	0.3581	0.1062	-0.1259	0.0055	0.1468	-0.0101	0.0419	0.1227	0.0046	0.1057	42.3591	79.9289	13.1038
21	3.6702	0.1486	0.4092	5.0969	-1.6303	2.6595	0.1731	0.395	0.2724	-0.1371	-0.2168	0.182	-0.5636	0.0474	-0.027	0.1301	0.0233	0.0043	0.1361	0.0804	0.1508	45.546	88.846	-5.7712

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:12)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 13:24)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 25:35)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 36:62)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 63:72)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 73:85)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 86:129)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 130:141)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 142:159)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 1:17)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 18:24)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 25:32)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 33:39)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 40:52)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 53:60)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 61:73)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 74:83)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 84:99)
19	X-RAY DIFFRACTION	19	chain 'B' and (resseq 100:113)
20	X-RAY DIFFRACTION	20	chain 'B' and (resseq 114:120)
21	X-RAY DIFFRACTION	21	chain 'B' and (resseq 121:128)

-
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