PDB-4eiz: Structure of Nb113 bound to apoDHFR

ID or keywords:

Entry

Database: PDB / ID: 4eiz

Title

Structure of Nb113 bound to apoDHFR

Components

Dihydrofolate reductase
Nb113 Camel antibody fragment

Keywords

OXIDOREDUCTASE/IMMUNE SYSTEM / NADP BINDING / OXIDOREDUCTASE-IMMUNE SYSTEM complex

Function / homology

Function and homology information

methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4eiz.cif.gz	238 KB	Display	PDBx/mmCIF format
PDB format	pdb4eiz.ent.gz	202.8 KB	Display	PDB format
PDBx/mmJSON format	4eiz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4eiz_validation.pdf.gz	442 KB	Display	wwPDB validaton report
Full document	4eiz_full_validation.pdf.gz	445.9 KB	Display
Data in XML	4eiz_validation.xml.gz	25.7 KB	Display
Data in CIF	4eiz_validation.cif.gz	36.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/4eiz ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eiz	HTTPS FTP

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Related structure data

Related structure data	4eigC 4ej1C 4fhbC C: citing same article (ref.)
Similar structure data	4yhd-4 4q1q-2 4p91-d 4ej1-2 1g2c-2 4yhd-1 4yhd-6 1ng1-d 1pvl-d 6nwo-2 1jpn-2 6u3f-d 4yhd-5 6lea-2 1lkf-d 2j46-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4eigC

4ej1C

4fhbC

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	#34 - Oct 2002 Dihydrofolate Reductase similarity (9) #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 Camel antibody fragment

D: Nb113 Camel antibody fragment

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

1

A: Dihydrofolate reductase

D: Nb113 Camel antibody fragment

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

2

B: Dihydrofolate reductase

C: Nb113 Camel antibody fragment

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

Unit cell

Length a, b, c (Å)	101.361, 77.517, 93.473
Angle α, β, γ (deg.)	90.00, 91.28, 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 Camel 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.8 Å³/Da / Density % sol: 56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 25.5% PEG4000, 0.085M NaCitrate, 0.17 M Ammonium Sulphate, 25% Glycerol, pH 5.6, 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: 0.978 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2007
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.2→20 Å / Num. all: 36808 / Num. obs: 35739 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.2→2.5 Å / % possible all: 97.1

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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: 2.2→19.989 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2242	1772	4.96 %
R_work	0.1705	-	-
obs	0.1733	35718	96.96 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.329 Å² / k_sol: 0.368 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.5217 Å²	0 Å²	10.8113 Å²
2-	-	4.819 Å²	0 Å²
3-	-	-	-2.2973 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→19.989 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4432	0	0	358	4790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4544
X-RAY DIFFRACTION	f_angle_d	1.106	6169
X-RAY DIFFRACTION	f_dihedral_angle_d	13.239	1619
X-RAY DIFFRACTION	f_chiral_restr	0.076	658
X-RAY DIFFRACTION	f_plane_restr	0.006	803

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 (%)
2.2-2.2587	0.253	113	0.1831	2573	X-RAY DIFFRACTION	97
2.2587-2.325	0.2591	130	0.1856	2610	X-RAY DIFFRACTION	97
2.325-2.3999	0.2834	128	0.1927	2585	X-RAY DIFFRACTION	97
2.3999-2.4856	0.2721	150	0.1851	2615	X-RAY DIFFRACTION	97
2.4856-2.5849	0.2534	117	0.1837	2614	X-RAY DIFFRACTION	97
2.5849-2.7023	0.297	125	0.1907	2597	X-RAY DIFFRACTION	97
2.7023-2.8444	0.2951	109	0.1962	2636	X-RAY DIFFRACTION	97
2.8444-3.022	0.2521	148	0.1864	2616	X-RAY DIFFRACTION	97
3.022-3.2544	0.2612	165	0.1879	2567	X-RAY DIFFRACTION	97
3.2544-3.5802	0.2048	151	0.1709	2613	X-RAY DIFFRACTION	97
3.5802-4.0944	0.1954	133	0.1501	2641	X-RAY DIFFRACTION	98
4.0944-5.144	0.1637	150	0.127	2612	X-RAY DIFFRACTION	97
5.144-19.9896	0.1999	153	0.1791	2667	X-RAY DIFFRACTION	97

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	6.6637	-5.0483	-0.8539	5.7924	2.0555	1.7479	-0.0107	0.5444	-0.0816	0.0747	-0.2752	0.3059	-0.0515	-0.4366	0.1314	0.1265	-0.026	-0.0237	0.178	-0.0044	0.1047	65.7549	-21.4092	11.5038
2	3.2318	-2.9212	-1.4292	2.5868	1.3878	1.2348	0.1596	0.2149	0.4392	-0.1677	-0.0525	-0.2374	-0.0409	0.0232	-0.1171	0.1205	0.0261	-0.02	0.1055	0.0315	0.1553	73.6792	-16.6471	10.1799
3	3.2102	-1.613	-1.8867	8.5569	-1.8012	4.7024	0.1953	0.3899	0.2746	-0.1684	-0.0266	-0.1265	-0.4794	-0.1224	-0.1088	0.213	0.0086	0.0256	0.2276	-0.0106	0.137	79.9729	-23.8386	-0.667
4	5.9483	-2.2578	-2.04	2.0218	1.3772	1.8487	-0.3955	0.238	-0.8845	0.1801	0.1606	0.2706	0.2721	-0.1476	0.1812	0.2116	0.0375	0.0112	0.1769	0.0111	0.2169	72.8069	-28.1863	11.6649
5	5.0245	-2.2856	-0.3239	4.056	0.4142	2.6651	-0.3334	-0.0536	-0.3573	0.2815	0.0859	0.1969	0.4297	-0.1122	0.1352	0.1832	0.0427	0.0578	0.1753	0.0235	0.1404	64.2936	-21.6153	19.8509
6	3.6408	-2.1486	-1.8902	2.0546	1.0302	7.5329	0.1113	0.0867	-0.0164	-0.0744	-0.1007	0.1165	0.0651	-0.0234	-0.0328	0.1237	0.0126	-0.042	0.1026	-0.0114	0.1358	35.8142	12.3508	36.3703
7	2.4226	-1.5427	-2.2293	4.7819	4.0599	6.1941	-0.05	-0.4589	0.0034	0.0871	-0.0201	0.047	0.1246	0.0645	0.0523	0.1821	0.0435	-0.035	0.1852	0.0096	0.1724	39.3972	4.4054	42.4217
8	8.7196	-0.4482	0.712	6.1181	-0.2572	5.6551	-0.1248	0.481	-0.5478	-0.1963	0.1015	0.5069	0.2144	-0.1313	-0.0279	0.1788	0.0256	0.0492	0.1634	-0.0591	0.2362	26.9347	10.7166	46.5372
9	8.3417	-1.8965	-0.7424	6.177	-0.8045	3.5501	0.0072	0.0894	-0.9126	0.4244	-0.0305	1.0073	0.1545	-0.2805	-0.0116	0.1896	-0.0004	0.0365	0.2173	-0.0236	0.3527	21.7579	11.0325	50.1661
10	7.1157	0.1594	-2.1957	5.2339	0.2653	4.447	0.0708	0.0711	0.5288	0.3291	0.0231	0.4949	-0.3243	-0.177	-0.2261	0.2032	0.046	0.115	0.2041	-0.0731	0.2944	22.4548	21.5759	49.5166
11	3.9759	-0.32	-0.5008	3.7432	-0.418	4.6645	0.1925	0.2582	0.5975	-0.1632	-0.1008	0.1457	-0.724	-0.1844	-0.0632	0.1752	0.0899	-0.003	0.1575	-0.0472	0.2188	31.7428	20.5218	44.2978
12	2.8904	-1.7619	-0.4577	3.6689	0.473	3.5387	0.1726	0.3033	0.1093	-0.2415	-0.2544	0.2428	-0.2513	-0.4741	-0.0079	0.1023	-0.0038	-0.0218	0.1934	0.0083	0.1621	38.479	13.1276	33.942
13	3.9078	0.158	-0.142	4.5794	1.2248	3.4879	0.046	0.1855	0.2706	0.0656	0.0428	-0.2172	-0.2971	0.457	-0.0314	0.1438	0.0024	-0.016	0.1622	0.0224	0.0699	46.5363	13.8056	37.8152
14	6.0568	0.0145	-0.6119	4.1029	-0.1716	1.2953	0.1025	-0.3114	0.1454	0.5489	0.2363	-0.678	0.3913	0.3241	-0.5015	0.0751	0.0077	-0.026	0.1882	0.0687	0.0878	64.9828	5.3393	12.2931
15	5.4771	-0.7397	-3.2237	4.0518	0.868	4.0924	0.1143	-0.8322	0.1553	0.3157	0.0907	-0.2602	-0.4324	0.3879	-0.1118	0.2415	0.006	-0.0581	0.195	0.0309	0.1873	63.258	5.5211	18.9
16	7.1182	-1.8033	-5.8871	3.512	-0.9023	6.7409	0.5187	-1.0163	0.5607	0.4599	-0.1341	-0.9389	-0.5423	1.3846	-0.5265	0.2739	-0.047	-0.0354	0.2613	-0.0171	0.2403	55.3474	13.3653	28.7921
17	3.4125	-1.8277	0.8671	3.3202	-0.7611	3.0809	0.4205	1.0998	1.0444	-0.9286	-0.3229	-0.5383	-0.5334	0.1129	0.4322	0.3838	0.2706	0.0098	-0.1106	0.396	0.1724	56.4896	13.3767	8.8714
18	1.676	-0.196	-1.7651	2.0243	0.9186	2.0657	-0.0833	-0.0495	-0.0717	-0.0035	-0.037	-0.0224	0.1257	0.1816	0.0696	0.076	0.0416	-0.0502	0.0789	0.0145	0.0694	51.4472	4.0023	17.3744
19	2.0221	-0.6133	-2.576	2.3917	1.6038	3.619	0.081	-0.0951	0.0792	-0.1367	-0.0104	-0.1198	-0.0161	-0.0178	-0.0494	0.1429	0.0218	-0.0331	0.1217	0.0199	0.144	58.6619	5.3715	11.6009
20	1.6718	-0.2277	-2.1094	1.4468	0.4487	2.99	0.4046	-0.0128	0.3289	-0.2738	-0.1968	-0.025	-0.5069	-0.0866	-0.1956	0.2202	0.0674	-0.0225	0.156	0.0229	0.1926	47.3976	15.5264	19.8654
21	4.546	-2.8948	-3.9466	1.9917	2.4899	3.4155	0.0833	0.0669	0.3974	-0.2297	0.2796	0.0599	-0.447	0.469	-0.4498	0.2597	-0.0115	0.0561	0.1263	0.058	0.2122	65.0881	7.1851	6.1224
22	3.9977	0.4102	-1.9326	3.249	0.8051	5.2131	-0.6658	-0.7035	-0.1821	0.7917	0.5996	0.0906	0.3233	0.0141	0.1422	0.1664	-0.044	0.0714	0.2221	0.0753	0.1855	38.4928	-14.6354	37.7784
23	8.2018	-6.9093	2.4734	9.2538	-1.4729	6.202	-0.0821	-1.0927	-0.3144	-0.0284	0.3764	-0.0191	0.3972	0.6394	-0.2334	0.2172	0.0783	0.0604	0.3025	0.0115	0.2583	45.2704	-14.4181	36.6445
24	7.7524	0.8968	-2.2237	2.485	0.9383	2.6938	-0.4686	-0.8896	-0.7093	0.3031	0.0656	0.0547	0.6617	-0.0196	0.0892	0.3186	0.0242	0.1488	0.1267	0.105	0.2824	48.271	-21.2262	29.5606
25	7.2598	5.9703	-5.3669	4.9112	-4.4184	3.9699	-0.6811	0.265	-0.4571	-0.108	0.2254	0.6699	1.0337	-0.6457	0.1581	0.3356	-0.1637	0.2327	0.3326	-0.1111	0.544	35.698	-22.7242	27.2008
26	4.1584	-3.4202	-1.6485	4.6826	0.2215	1.3296	-0.0442	0.7921	0.1004	-0.1401	-0.0738	0.1785	0.1282	-0.5223	0.1103	0.1517	-0.018	-0.037	0.3243	0.0563	0.1714	43.5304	-13.0573	21.4798
27	8.6288	-1.7099	-1.1832	4.6601	-0.3279	4.3609	-0.5683	-0.267	0.2507	0.3835	0.3108	-0.1317	0.0151	0.3955	0.2483	0.1776	0.0427	-0.0145	0.1628	0.0086	0.1374	47.6745	-11.8981	31.4539
28	4.9951	-1.9916	-3.3617	4.792	1.1218	2.275	-0.3366	0.7464	-0.3961	0.3431	-0.015	0.2445	0.352	-0.3799	0.2676	0.2221	-0.0789	0.0315	0.2372	0.0224	0.3125	34.8784	-16.4706	30.7589
29	3.312	-0.0929	-2.1503	1.8926	0.4473	1.48	-0.6735	0.21	-1.0289	0.3522	-0.2985	0.5991	0.4093	-0.4727	0.4084	0.3046	-0.1219	0.1699	0.2571	-0.1073	0.5032	48.4387	-25.2823	21.883
30	7.5136	-3.6397	-5.3993	7.7298	4.0278	4.207	-0.3822	-0.5607	-0.1113	-0.1146	0.5867	-0.1191	0.1131	-0.1198	-0.2571	0.2387	-0.0434	0.1138	0.1971	0.0324	0.3208	32.4914	-16.6783	37.4815

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 20:48)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 49:85)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 86:115)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 116:159)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 1:19)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 20:35)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 36:50)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 51:72)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 73:85)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 86:106)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 107:125)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 126:159)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 2:17)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 18:25)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 26:33)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 34:45)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 46:76)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 77:99)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 100:118)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ 119:128)
22	X-RAY DIFFRACTION	22	CHAIN D AND (RESSEQ 2:17)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 18:25)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 26:39)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 40:51)
26	X-RAY DIFFRACTION	26	CHAIN D AND (RESSEQ 52:67)
27	X-RAY DIFFRACTION	27	CHAIN D AND (RESSEQ 68:83)
28	X-RAY DIFFRACTION	28	CHAIN D AND (RESSEQ 84:99)
29	X-RAY DIFFRACTION	29	CHAIN D AND (RESSEQ 100:118)
30	X-RAY DIFFRACTION	30	CHAIN D AND (RESSEQ 119:128)

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Yorodumi