PDB-4i1n: R104A-ca1697 nanobody binding to the binary DHFR.folate complex

ID or keywords:

Entry

Database: PDB / ID: 4i1n

Title

R104A-ca1697 nanobody binding to the binary DHFR.folate complex

Components

Dihydrofolate reductase
Protein ca1697 (nanobody)

Keywords

OXIDOREDUCTASE/IMMUNE SYSTEM / alpha/beta fold / immunoglobulin fold / reductase / NADPH / folate derivatives / hydride transfer / 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 / folic acid metabolic process / dihydrofolate reductase ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

lama glama (llama)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.888 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 21, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 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 / _pdbx_entry_details.has_protein_modification / _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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PDBx/mmCIF format	4i1n.cif.gz	134.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4i1n_validation.pdf.gz	745.2 KB	Display	wwPDB validaton report
Full document	4i1n_full_validation.pdf.gz	746.7 KB	Display
Data in XML	4i1n_validation.xml.gz	16.2 KB	Display
Data in CIF	4i1n_validation.cif.gz	23.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/4i1n ftp://data.pdbj.org/pub/pdb/validation_reports/i1/4i1n	HTTPS FTP

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Related structure data

Related structure data	4i13C C: citing same article (ref.)
Similar structure data	4i13-d 5eer-d 3ewi-d 3n3w-d 5ees-d 6dfd-d 2nzj-5 7nbi-d 3pa1-2 4l4w-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

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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: Protein ca1697 (nanobody)

hetero molecules

33.2 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)	49.267, 55.642, 119.213
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: 14740.489 Da / Num. of mol.: 1 / Mutation: R104A 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.: 1 / Source method: obtained synthetically / Formula: C₁₉H₁₉N₇O₆
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	RESIDUE 104 ALA OF ENTITY 2 REPRESENT ENGINEERED MUTATION (R104A)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% v/v PEG 200, 5% w/v PEG 3000, 100mM MES Sodium Salt, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 13, 2012
Radiation	Monochromator: graded multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.888→20 Å / Num. all: 26802 / Num. obs: 26266 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / B_iso Wilson estimate: 23.23 Å²
Reflection shell	Resolution: 1.9→1.93 Å / % possible all: 98.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.888→19.596 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8347 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2139	1318	5.05 %
R_work	0.1773	-	-
obs	0.1793	26116	96.53 %
all	-	26266	-

Solvent computation

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

Displacement parameters

B_iso max: 96.04 Å² / B_iso mean: 28.294 Å² / B_iso min: 6.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.8755 Å²	-0 Å²	0 Å²
2-	-	-5.1182 Å²	-0 Å²
3-	-	-	1.2426 Å²

Refinement step

Cycle: LAST / Resolution: 1.888→19.596 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2233	0	32	302	2567

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2343
X-RAY DIFFRACTION	f_angle_d	1.103	3189
X-RAY DIFFRACTION	f_dihedral_angle_d	14.52	850
X-RAY DIFFRACTION	f_chiral_restr	0.073	341
X-RAY DIFFRACTION	f_plane_restr	0.005	414

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8878-1.9634	0.2562	121	0.2134	2472	2593	88
1.9634-2.0526	0.2921	128	0.1965	2791	2919	98
2.0526-2.1607	0.2359	148	0.1809	2745	2893	98
2.1607-2.2959	0.2206	142	0.1842	2791	2933	99
2.2959-2.4728	0.2408	157	0.1915	2779	2936	98
2.4728-2.7211	0.2537	145	0.1905	2787	2932	98
2.7211-3.1135	0.2202	177	0.184	2793	2970	98
3.1135-3.9175	0.1926	147	0.1647	2804	2951	97
3.9175-19.5967	0.1764	153	0.1622	2836	2989	94

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	8.1552	-0.3737	-3.1112	2.5426	-0.0358	5.162	-0.4248	-0.3023	-0.3172	0.4616	0.0832	-0.4703	0.3325	0.2065	0.2921	0.2784	0.0274	-0.0652	0.1543	0.0177	0.2093	47.9964	45.2813	20.753
2	0.2425	0.4229	-0.1473	1.9112	0.4687	0.5385	0.1244	0.0046	-0.142	0.0736	0.0179	-0.1466	-0.1156	-0.0513	-0.1033	0.2381	0.0267	-0.051	0.1907	0.0446	0.2699	50.6207	55.7528	12.8461
3	7.4213	-1.1146	-3.2897	3.1288	-2.1296	7.2683	-0.0951	0.1836	-0.2339	-0.349	-0.0043	0.2452	0.3183	-0.3157	0.158	0.1876	-0.0245	-0.0318	0.1881	0.0033	0.1693	40.3304	45.949	9.9457
4	2.1823	-0.3415	-0.671	2.9608	-0.1836	2.1977	-0.0185	-0.0724	0.0276	0.7904	-0.0673	0.62	0.009	-0.3478	0.0346	0.2929	-0.0097	0.1028	0.2277	0.0196	0.231	33.7474	54.3847	23.2749
5	0.4351	-0.6799	-0.3817	1.1858	1.0426	1.8428	0.0976	-0.1074	-0.0063	0.7616	-0.0379	-0.2809	0.0938	-0.1224	-0.0963	0.44	-0.0142	-0.0169	0.1831	0.0168	0.1442	44.8278	44.8808	24.543
6	2.73	0.6939	-1.1806	1.8358	-0.476	2.6937	-0.0997	0.0057	0.1243	0.6507	-0.0227	-0.8213	0.1939	0.3661	0.1716	0.3551	0.0582	-0.1405	0.248	0.0035	0.3505	55.5235	48.9092	21.519
7	1.2444	0.3486	-0.8966	0.5996	-0.7657	5.204	-0.1033	0.0016	0.0773	0.5266	0.2592	-0.2878	0.1887	-0.0912	-0.0948	0.4079	0.0387	-0.054	0.1871	0.0035	0.2126	49.847	35.0875	17.1533
8	1.1227	0.62	-0.0012	3.0917	0.2293	1.7275	-0.1125	0.0976	-0.0097	-0.1686	0.2079	-0.3832	0.4848	-0.2242	-0.089	0.2524	0.0091	0.0024	0.1693	0.0293	0.1878	49.7094	41.7503	10.7884
9	1.3018	0.3554	-0.5424	1.8277	-1.1316	8.1301	-0.1605	0.085	0.2612	0.1514	0.0013	0.0756	-0.3423	0.3785	0.1877	0.1139	0.0013	-0.0168	0.1755	0.029	0.2476	49.2897	82.6944	1.2716
10	0.7359	0.337	0.297	0.6363	-0.2886	2.0063	-0.1048	0.0009	0.0701	-0.064	-0.1647	-0.1243	-0.0469	0.4512	0.2634	0.1792	-0.0055	-0.0065	0.2359	0.0836	0.2841	53.0374	79.2729	3.505
11	1.204	0.0313	0.2102	2.3939	-0.2492	2.6434	-0.0535	-0.1288	0.0827	0.2795	0.1175	-0.073	-0.2424	-0.1377	-0.0376	0.1219	0.0182	-0.0004	0.1603	0.038	0.1733	48.0213	72.8704	11.5779
12	4.8775	-3.2428	1.2557	3.1248	-0.5442	0.3829	-0.2271	0.191	0.3736	0.0657	0.1253	0.1318	-0.105	-0.1325	0.101	0.1268	-0.0038	0.0015	0.1993	0.0699	0.2684	38.9803	74.1963	1.522
13	2.564	0.8825	0.4918	1.599	1.236	2.9445	-0.2512	0.2997	0.2074	0.1994	-0.0549	-0.2021	0.128	0.371	0.2914	0.1232	0.0309	-0.0156	0.1416	0.0192	0.2213	50.9957	65.0141	5.9266
14	1.5123	-1.0569	0.4987	2.135	-0.5294	4.7273	0.0203	-0.0484	-0.1236	-0.0236	0.1324	-0.0483	0.1071	-0.0082	-0.138	0.0907	-0.0059	0.0053	0.1923	0.0378	0.1917	51.6966	71.7501	1.033
15	1.6574	-0.5211	-0.185	1.7128	-2.3561	3.7575	-0.0813	0.2233	0.1535	-0.1533	0.1943	0.0198	0.1138	-0.4788	-0.1409	0.1464	-0.0415	-0.0251	0.214	0.0548	0.2565	43.7186	77.8613	-2.771
16	5.2882	-0.5904	0.0129	5.8408	0.6508	4.5534	-0.1192	-0.3449	0.1775	0.0554	0.1219	0.688	-0.0918	-0.5265	0.0071	0.1405	0.0062	0.0177	0.2328	0.0426	0.2535	39.2641	66.8932	9.8149
17	9.0045	3.2732	-0.3867	3.6365	-2.9485	3.2417	0.0201	-0.6085	0.4753	0.1722	-0.1436	0.4621	-0.2191	-0.1926	0.2765	0.2233	-0.0081	0.0059	0.2831	-0.0112	0.2682	41.4027	78.5368	12.416
18	7.842	-0.1026	0.6455	7.4714	2.8208	1.9719	-0.0781	0.7383	0.5762	-0.59	0.0599	0.0725	-0.4859	-0.4116	0.0183	0.197	-0.0276	-0.0423	0.3112	0.1068	0.3168	44.0778	85.4528	-7.5465

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 36:96)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 97:115)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 116:129)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 130:141)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 142:159)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 1:17)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 18:24)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 25:39)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 40:52)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 53:60)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 61:83)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 84:99)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 100:113)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 114:120)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 121:128)

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