PDB-4ej1: Binding of Nb113 camelid antibody fragment with the binary DHFR:f...

ID or keywords:

Entry

Database: PDB / ID: 4ej1

Title

Binding of Nb113 camelid antibody fragment with the binary DHFR:folate complex

Components

Dihydrofolate reductase
Nb113 camelid antibody fragment

Keywords

Oxidoreductase/Immune system / FOLATE / Oxidoreductase-Immune system complex

Function / homology

Function and homology information

methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic 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: 1.75 Å

Authors

Oyen, D. / Srinivasan, V.

Citation

Journal: Biochim.Biophys.Acta / Year: 2013
Title: Mechanistic analysis of allosteric and non-allosteric effects arising from nanobody binding to two epitopes of the dihyrofolate reductase of Escherichia coli.
Authors: Oyen, D. / Wechselberger, R. / Srinivasan, V. / Steyaert, J. / Barlow, J.N.

History

Deposition	Apr 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2013	Group: Database references
Revision 1.2	Sep 4, 2013	Group: Database references
Revision 1.3	Oct 30, 2013	Group: Derived calculations
Revision 1.4	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ej1.cif.gz	252.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ej1.ent.gz	206.3 KB	Display	PDB format
PDBx/mmJSON format	4ej1.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/ej/4ej1 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/4ej1	HTTPS FTP

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Related structure data

Related structure data	4eigC 4eizC 4fhbC C: citing same article (ref.)
Similar structure data	6ulv-1 4fhb-d 4q1q-1 1xja-1 4qw2-2 6y31-3 1jpn-2 2j46-1 4eiz-1 6nx3-3 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

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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: Dihydrofolate reductase

C: Nb113 camelid antibody fragment

D: Nb113 camelid antibody fragment

hetero molecules

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

1

A: Dihydrofolate reductase

D: Nb113 camelid antibody fragment

hetero molecules

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

2

B: Dihydrofolate reductase

C: Nb113 camelid antibody fragment

hetero molecules

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

Unit cell

Length a, b, c (Å)	100.741, 77.064, 92.777
Angle α, β, γ (deg.)	90.00, 92.00, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Dihydrofolate reductase Mass: 18019.340 Da / Num. of mol.: 2 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	Nb113 camelid antibody fragment Mass: 14815.256 Da / Num. of mol.: 2 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 Mass: 441.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₁₉N₇O₆
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.74 Å³/Da / Density % sol: 55.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 30% PEG1000, 100 mM phosphate/citrate, 110 mM Lithium Citrate, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2008
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0723 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. all: 76010 / Num. obs: 72438 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 1.75→1.774 Å / % possible all: 95.3

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→19.863 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 26.71 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2235	3430	5.02 %
R_work	0.1864	-	-
obs	0.1883	68339	95.66 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 45.645 Å² / k_sol: 0.367 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.0354 Å²	-0 Å²	-0.5145 Å²
2-	-	-0 Å²	0 Å²
3-	-	-	-0.0354 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→19.863 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4453	0	88	529	5070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4651
X-RAY DIFFRACTION	f_angle_d	1.114	6313
X-RAY DIFFRACTION	f_dihedral_angle_d	14.64	1661
X-RAY DIFFRACTION	f_chiral_restr	0.079	656
X-RAY DIFFRACTION	f_plane_restr	0.004	816

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 (%)
1.75-1.774	0.3933	112	0.3451	2444	X-RAY DIFFRACTION	91
1.774-1.7993	0.3365	121	0.3212	2515	X-RAY DIFFRACTION	92
1.7993-1.8261	0.3797	141	0.2971	2512	X-RAY DIFFRACTION	93
1.8261-1.8546	0.2727	118	0.2968	2557	X-RAY DIFFRACTION	93
1.8546-1.885	0.3576	119	0.286	2527	X-RAY DIFFRACTION	94
1.885-1.9175	0.3505	144	0.2753	2555	X-RAY DIFFRACTION	94
1.9175-1.9523	0.3141	132	0.2612	2513	X-RAY DIFFRACTION	94
1.9523-1.9899	0.2858	123	0.2442	2588	X-RAY DIFFRACTION	95
1.9899-2.0304	0.3164	133	0.2371	2568	X-RAY DIFFRACTION	95
2.0304-2.0745	0.246	132	0.2169	2569	X-RAY DIFFRACTION	94
2.0745-2.1227	0.2643	123	0.2152	2568	X-RAY DIFFRACTION	95
2.1227-2.1758	0.236	137	0.2049	2574	X-RAY DIFFRACTION	95
2.1758-2.2345	0.2485	143	0.1939	2577	X-RAY DIFFRACTION	96
2.2345-2.3002	0.2273	152	0.1939	2550	X-RAY DIFFRACTION	95
2.3002-2.3743	0.2215	138	0.2004	2602	X-RAY DIFFRACTION	95
2.3743-2.459	0.2372	149	0.2027	2575	X-RAY DIFFRACTION	96
2.459-2.5573	0.2642	148	0.2049	2602	X-RAY DIFFRACTION	96
2.5573-2.6734	0.2453	142	0.2011	2605	X-RAY DIFFRACTION	96
2.6734-2.814	0.242	154	0.2032	2623	X-RAY DIFFRACTION	97
2.814-2.9897	0.2291	156	0.1981	2671	X-RAY DIFFRACTION	98
2.9897-3.2197	0.2374	135	0.1885	2699	X-RAY DIFFRACTION	99
3.2197-3.542	0.1999	136	0.1642	2722	X-RAY DIFFRACTION	99
3.542-4.0508	0.197	138	0.1421	2707	X-RAY DIFFRACTION	99
4.0508-5.0893	0.1509	141	0.1245	2725	X-RAY DIFFRACTION	99
5.0893-19.8642	0.1778	163	0.1718	2761	X-RAY DIFFRACTION	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	7.5512	3.8067	-1.72	3.2961	-1.9151	4.0456	-0.126	-0.349	0.4306	-0.0325	-0.1464	0.1086	-0.0829	0.3674	0.2942	0.202	0.0033	-0.0517	0.2478	-0.0393	0.2203	33.8917	59.8717	34.7903
2	3.9787	5.3811	-2.9631	9.2452	-2.5522	3.2127	-0.0275	0.0042	0.7101	-0.001	0.0688	0.3665	-0.0827	-0.1873	-0.0394	0.1996	-0.0251	-0.0209	0.2062	-0.0762	0.2574	28.5113	68.0259	31.215
3	8.3922	-0.5052	2.009	7.949	-0.1803	7.111	0.1123	-0.3538	0.4761	0.5979	-0.1113	0.0047	-0.3443	0.5112	0.0157	0.225	-0.0847	0.03	0.258	-0.0106	0.1711	23.7743	61.3741	42.923
4	2.5082	-1.3505	2.2789	8.8234	-0.9875	2.3767	-0.0233	-0.3845	0.7198	0.7018	-0.1551	0.0507	-0.4677	0.1076	0.044	0.2844	0.0069	0.0366	0.2647	-0.0332	0.2906	19.0937	62.6493	42.6619
5	6.543	-0.4111	-0.1977	7.925	-0.5087	6.5977	0.0746	-0.9572	-0.0549	1.2784	0.2405	-0.2397	-0.0485	0.324	-0.2971	0.3129	-0.0033	-0.02	0.3513	0.0094	0.1709	19.9827	54.7261	49.4629
6	6.6636	4.5525	-2.8408	4.3007	-1.4206	3.0922	-0.4379	-0.1057	-0.5361	-0.2916	0.1233	-0.2901	0.5824	-0.1105	0.2585	0.2359	-0.0015	-0.0102	0.2095	-0.0131	0.212	26.9161	53.1984	34.6177
7	5.0931	2.0954	-0.8508	5.8153	-1.4901	3.6096	-0.2489	0.0147	-0.3663	-0.1263	0.1319	-0.3569	0.3303	0.1896	0.0584	0.2012	-0.0028	0.0371	0.2236	-0.0464	0.1898	35.3043	59.5893	26.415
8	6.4288	4.805	-4.6392	7.393	-4.758	3.7525	0.2547	-0.002	0.3424	0.2074	-0.1486	0.0464	-0.417	-0.052	-0.1995	0.1819	0.0107	-0.0358	0.1565	0.0162	0.1892	61.6322	97.1654	9.0869
9	7.9414	7.2891	1.9758	7.0144	1.489	0.7405	-0.6094	0.7706	-0.9514	-1.0696	0.6413	-0.6194	-0.0982	0.8146	0.0655	0.3633	-0.0646	0.0546	0.3673	-0.0795	0.3131	65.3246	84.5866	12.2215
10	3.6986	2.1631	-2.7536	3.9788	-0.6034	2.977	-0.169	-0.1296	-0.3267	-0.2899	-0.0402	-0.3188	0.2975	0.0576	0.1913	0.2318	0.0163	0.0156	0.1895	0.0611	0.1912	67.264	90.1285	0.2815
11	6.9928	2.773	-1.6195	5.6677	0.2347	3.9071	-0.1547	-0.1128	-0.6971	-0.4327	-0.0377	-0.9285	0.2909	0.5334	0.2184	0.3021	0.0796	0.081	0.2819	0.0729	0.384	77.8037	91.8615	-3.1396
12	7.1963	1.3628	-1.9611	8.2213	-0.5454	5.543	0.1485	-0.0511	0.4429	-0.1116	-0.014	-0.5085	-0.2872	0.1516	-0.1411	0.2308	-0.0347	0.0765	0.2522	0.0566	0.3187	77.4128	102.7943	-2.6921
13	3.68	1.8739	-2.3752	3.6231	-1.495	4.4576	0.32	-0.1157	0.2411	0.1342	-0.3078	-0.1505	-0.2943	0.4758	0.0226	0.1747	-0.0225	-0.0254	0.1983	0.0095	0.2345	64.7733	98.18	7.4066
14	3.4785	2.0671	1.7462	3.1941	-1.5628	4.3807	-0.0947	-0.1887	0.7273	0.4154	-0.0952	0.261	-0.4651	-0.3213	0.27	0.3459	0.0486	-0.0006	0.3487	-0.0565	0.349	53.0275	100.43	9.4215
15	5.2244	0.1574	-0.2359	7.5804	-3.1231	5.7588	-0.0197	-0.1346	0.0665	-0.3882	0.3256	0.5433	0.1078	-0.4308	-0.2614	0.1744	-0.0523	-0.0112	0.2524	-0.0436	0.1217	53.3625	90.3588	8.1351
16	0.7333	1.0732	-1.2245	3.0276	-2.8397	4.3117	0.1604	0.1141	0.087	-0.0423	0.105	0.2915	0.0194	-0.616	-0.2949	0.2709	0.0114	0.0576	0.3033	-0.0113	0.2856	34.1176	85.7247	34.9261
17	2.2559	-1.7583	-0.2438	8.4707	-6.5869	6.5665	0.1643	0.3504	-0.0572	-0.2268	0.2692	0.7025	-0.2836	-0.5605	-0.3229	0.3328	-0.036	-0.0149	0.248	-0.0189	0.2794	36.4776	85.7973	28.4446
18	4.5365	-0.0625	-4.5929	5.9124	-1.1934	4.9046	0.6392	1.2136	-0.2175	-0.0515	-0.0045	1.4195	-0.8494	-1.9298	-0.7224	0.4097	0.1007	0.0152	0.5692	-0.0199	0.4411	43.3108	94.568	17.6016
19	4.6837	-0.9007	-1.4774	4.4006	2.4949	6.0327	0.2773	-1.0555	0.9227	0.5642	-0.1656	0.4808	-0.8993	0.392	-0.1204	0.4229	-0.133	0.0534	0.3097	-0.1322	0.3143	43.4424	94.427	38.6463
20	2.6479	0.409	-3.0238	1.3048	-0.9025	3.6072	0.1038	-0.0226	0.0295	0.0918	-0.0384	0.0618	-0.2517	0.1041	-0.0476	0.2267	-0.0445	-0.059	0.1683	-0.0265	0.1745	46.8129	87.706	30.3965
21	4.6011	1.9017	-3.9708	2.2088	-1.537	4.8306	0.6151	-0.028	0.7122	0.2608	-0.1393	0.3533	-0.8852	-0.1158	-0.4332	0.3715	0.0001	0.054	0.1865	-0.0333	0.2692	40.6737	94.0549	34.7283
22	4.9826	5.7823	-3.0844	6.9722	-2.6273	7.0989	-1.3372	0.5055	-1.0084	-0.959	0.6533	-0.0346	0.7581	-0.6774	0.637	0.4131	-0.0347	0.2042	0.3032	-0.1209	0.4081	58.7137	64.2166	7.3612
23	1.9889	2.4298	-2.2376	4.1048	-1.4466	3.8525	-0.6166	0.8728	-0.8368	-0.654	0.7273	-0.7896	0.1879	0.3694	0.0743	0.2399	-0.0003	0.0712	0.2785	-0.1355	0.4107	60.8557	70.8543	10.8372
24	4.102	-0.9645	-3.208	2.8763	-0.4721	3.6053	-0.4404	0.2371	-0.6016	-0.3782	-0.0624	-0.485	0.7903	0.3944	0.2521	0.3928	0.0906	0.1684	0.2186	-0.0015	0.4267	55.0167	58.8042	16.1586
25	7.1642	1.5023	0.8772	2.7515	-1.3162	1.3495	-0.371	-1.3675	-0.0194	0.0667	-0.068	-0.3198	-0.0198	0.7153	0.3439	0.1891	0.0019	-0.0047	0.5151	-0.0032	0.2926	57.2849	65.9852	23.9185
26	8.5016	5.4731	-0.9239	7.8289	0.024	5.2971	-0.2643	0.2077	0.641	-0.2334	0.2689	0.3421	0.1129	-0.2201	0.0265	0.1566	-0.0068	-0.0082	0.1931	-0.0263	0.2233	52.0584	69.5477	15.0621
27	4.1069	2.9336	-3.4124	5.3217	-1.381	3.816	-0.2907	-1.3183	-0.1458	-0.2208	-0.1219	-0.4773	0.2246	0.6531	0.3152	0.2143	0.0511	0.0206	0.3678	-0.067	0.3831	64.7155	64.8529	15.7954
28	5.5906	0.8215	-4.607	0.4682	-0.7582	3.8493	-0.7452	-0.6331	-1.2337	-0.1627	-0.0142	-0.4141	0.5933	0.5812	0.6235	0.3119	0.0808	0.1285	0.3054	0.0644	0.4522	55.8415	58.648	19.9691

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:19)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 20:35)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 36:50)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 51:62)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 63:85)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 86:115)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 116:159)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 1:12)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 13:24)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 25:50)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 51:72)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 73:85)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 86:125)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 126:141)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 142:159)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 3:17)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 18:24)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 25:33)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 34:45)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 46:111)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ 112:128)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 3:12)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 13:24)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 25:44)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 45:67)
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESSEQ 68:83)
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESSEQ 84:99)
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESSEQ 100:128)

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