PDB-7rga: Crystal structure of nanoCLAMP3:VHH in complex with MTX

ID or keywords:

Entry

Database: PDB / ID: 7rga

Title

Crystal structure of nanoCLAMP3:VHH in complex with MTX

Components

nano CLostridial Antibody Mimetic Protein 3 VHH

Keywords

IMMUNE SYSTEM

Function / homology

METHOTREXATE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Guo, Z. / Alexandrov, K.

Funding support

Australia,

Canada, 4items

Organization	Grant number	Country
Australian Research Council (ARC)	DP160100973	Australia
Australian Research Council (ARC)	DP150100936	Australia
Canada Excellence Research Chair Award	CE200100029	Canada
National Health and Medical Research Council (NHMRC, Australia)	APP1113262	Australia

Citation

Journal: Nat Commun / Year: 2021
Title: Design of a methotrexate-controlled chemical dimerization system and its use in bio-electronic devices.
Authors: Guo, Z. / Smutok, O. / Johnston, W.A. / Walden, P. / Ungerer, J.P.J. / Peat, T.S. / Newman, J. / Parker, J. / Nebl, T. / Hepburn, C. / Melman, A. / Suderman, R.J. / Katz, E. / Alexandrov, K.

History

Deposition	Jul 14, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 6, 2022	Group: Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2	Oct 18, 2023	Group: Author supporting evidence / Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_audit_support / pdbx_initial_refinement_model Item: _pdbx_audit_support.country

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7rga.cif.gz	723.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7rga.ent.gz	603.3 KB	Display	PDB format
PDBx/mmJSON format	7rga.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/rg/7rga ftp://data.pdbj.org/pub/pdb/validation_reports/rg/7rga	HTTPS FTP

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Related structure data

Related structure data	7rg7C 2w1qS 3qxvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

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

Deposited unit

A: nano CLostridial Antibody Mimetic Protein 3 VHH

B: nano CLostridial Antibody Mimetic Protein 3 VHH

C: nano CLostridial Antibody Mimetic Protein 3 VHH

D: nano CLostridial Antibody Mimetic Protein 3 VHH

E: nano CLostridial Antibody Mimetic Protein 3 VHH

F: nano CLostridial Antibody Mimetic Protein 3 VHH

G: nano CLostridial Antibody Mimetic Protein 3 VHH

hetero molecules

232 kDa, 7 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)	173.200, 143.969, 181.814
Angle α, β, γ (deg.)	90.00, 94.34, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Antibody	nano CLostridial Antibody Mimetic Protein 3 VHH Mass: 32642.461 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-MTX / METHOTREXATE / Methotrexate Mass: 454.439 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂₀H₂₂N₈O₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 5.49 Å³/Da / Density % sol: 77.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.4 M sodium malonate-malonic acid pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95373 Å / Relative weight: 1
Reflection	Resolution: 2.9→48.38 Å / Num. obs: 1401844 / % possible obs: 100 % / Redundancy: 14.2 % / CC_1/2: 1 / Net I/σ(I): 7.5
Reflection shell	Resolution: 2.9→2.975 Å / Redundancy: 14.5 % / Num. unique obs: 70152 / CC_1/2: 1 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0110	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3QXV 2W1Q

3qxv

2w1q

Resolution: 2.9→48.38 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.92 / SU B: 29.507 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24223	4949	5 %	RANDOM
R_work	0.19469	-	-	-
obs	0.1971	93544	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 73.108 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.91 Å²	0 Å²	-0.42 Å²
2-	-	0.05 Å²	0 Å²
3-	-	-	-3.03 Å²

Refinement step

Cycle: 1 / Resolution: 2.9→48.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14416	0	245	3	14664

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.021	15080
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.057	1.956	20402
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.921	5	1846
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.741	24.003	717
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.713	15	2447
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.377	15	105
X-RAY DIFFRACTION	r_chiral_restr	0.137	0.2	2119
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	11686
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.949	1.5	9188
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.835	2	14655
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.421	3	5892
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.204	4.5	5747
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.387	330	-
R_work	0.34	6936	-
obs	-	-	99.99 %

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	0.3433	0.1601	0.1275	1.33	-0.0946	0.4673	0.019	-0.0414	0.0163	-0.0219	-0.0489	-0.0154	0.0782	-0.0164	0.0299	0.1354	-0.0211	-0.0236	0.1539	0.0252	0.0123	74.663	-15.884	28.524
2	0.538	-0.1985	-0.2	0.2712	-0.0511	1.4764	0.0136	-0.0604	0.0145	-0.0895	-0.0187	0.0016	0.1289	0.068	0.005	0.1121	0.0083	-0.0266	0.1507	0.0786	0.0548	107.899	-20.317	34.849
3	0.6452	-0.2939	-0.0485	1.6076	0.5681	0.5082	0.0642	-0.0341	0.107	-0.0265	-0.0686	-0.0474	0.0381	-0.0192	0.0044	0.0911	0.0178	-0.0103	0.1363	-0.0215	0.0324	54.033	9.485	12.175
4	1.9587	-0.095	-0.4329	0.4296	0.1046	0.2422	-0.0193	-0.128	0.1283	-0.1086	0.0102	0.0352	-0.0093	0.0265	0.0091	0.1658	-0.0687	-0.013	0.0953	-0.0237	0.026	120.314	17.75	20.659
5	0.4413	0.1532	-0.0377	0.42	-0.5071	2.26	0.0352	0.0413	0.0543	-0.0013	-0.0147	0.032	0.3031	0.0578	-0.0206	0.2459	0.0398	0.0624	0.0638	0.0374	0.0344	65.843	-53.56	70.026
6	0.5067	0.2188	-0.2651	1.4774	-1.1715	1.3168	-0.0142	-0.0002	0.0081	-0.0422	-0.0996	-0.2062	0.0382	0.0646	0.1139	0.0658	0.0464	0.0098	0.1647	0.1201	0.1136	136.563	-23.777	41.171
7	3.1629	0.9957	0.0429	0.4184	-0.019	0.7084	0.1202	-0.0165	0.5826	0.1311	-0.0165	0.2756	0.0982	0.1248	-0.1037	0.1039	0.0211	0.0967	0.0866	0.0426	0.265	62.445	-19.74	69.082
8	0.0828	0.0156	-0.037	0.066	0.0585	0.0772	-0.0646	-0.0636	-0.03	-0.0153	0.0099	0.0279	-0.0029	0.0696	0.0546	0.1547	0.0154	-0.0144	0.1991	0.0821	0.1023	88.558	-17.043	34.268
9	0.1132	0.0157	-0.0089	0.1085	0.0478	0.0364	-0.0363	0.0136	-0.0234	-0.062	0.0339	0.0257	0.0258	0.0564	0.0024	0.1575	0.0927	-0.0207	0.1748	0.0478	0.0711	91.377	-17.193	35.815
10	44.6654	7.7195	-40.8225	-3.4785	-6.7903	32.3783	-0.2924	5.8223	0.6583	0.4093	0.9191	0.0057	0.2616	-4.5845	-0.6266	0.3518	-0.0293	0.0081	1.0131	-0.0563	0.1698	85.415	-5.782	18.74

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 298
2	X-RAY DIFFRACTION	2	B	1 - 298
3	X-RAY DIFFRACTION	3	C	1 - 298
4	X-RAY DIFFRACTION	4	D	1 - 298
5	X-RAY DIFFRACTION	5	E	1 - 298
6	X-RAY DIFFRACTION	6	F	1 - 298
7	X-RAY DIFFRACTION	7	G	1 - 298
8	X-RAY DIFFRACTION	8	A	301
9	X-RAY DIFFRACTION	8	B	301
10	X-RAY DIFFRACTION	8	C	301
11	X-RAY DIFFRACTION	8	D	301
12	X-RAY DIFFRACTION	8	E	301
13	X-RAY DIFFRACTION	8	F	301
14	X-RAY DIFFRACTION	8	G	301
15	X-RAY DIFFRACTION	9	A	302 - 303
16	X-RAY DIFFRACTION	9	B	302 - 303
17	X-RAY DIFFRACTION	9	C	302 - 303
18	X-RAY DIFFRACTION	9	D	302 - 303
19	X-RAY DIFFRACTION	9	E	302 - 303
20	X-RAY DIFFRACTION	9	F	302 - 303
21	X-RAY DIFFRACTION	9	G	302 - 303
22	X-RAY DIFFRACTION	10	A	401 - 403

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