PDB-8fif: A2.3 Nanobody In Complex With Microcystin-LR

ID or keywords:

Entry

Database: PDB / ID: 8fif

Title

A2.3 Nanobody In Complex With Microcystin-LR

Components

Microcystin-LR
Single Domain Camelid Nanobody VHH A2.3

Keywords

IMMUNE SYSTEM / Nanobody

Function / homology

Microcystin-LR (MCLR) bound form

Function and homology information

Biological species

Lama glama (llama)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Arenas, R. / Tabares-da Rosa, S. / Gonzalez-Sapienza, G. / Wilson, D.K.

Funding support

1items

Citation

Journal: To Be Published
Title: A2.3 Nanobody In Complex With Microcystin-LR
Authors: Arenas, R. / Tabares-da Rosa, S. / Gonzalez-Sapienza, G. / Wilson, D.K.

History

Deposition	Dec 16, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8fif.cif.gz	96.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8fif.ent.gz	70.4 KB	Display	PDB format
PDBx/mmJSON format	8fif.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fif_validation.pdf.gz	479.7 KB	Display	wwPDB validaton report
Full document	8fif_full_validation.pdf.gz	500.1 KB	Display
Data in XML	8fif_validation.xml.gz	21.3 KB	Display
Data in CIF	8fif_validation.cif.gz	29 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/8fif ftp://data.pdbj.org/pub/pdb/validation_reports/fi/8fif	HTTPS FTP

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Related structure data

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	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Single Domain Camelid Nanobody VHH A2.3

B: Single Domain Camelid Nanobody VHH A2.3

C: Single Domain Camelid Nanobody VHH A2.3

D: Microcystin-LR

F: Microcystin-LR

G: Microcystin-LR

46.1 kDa, 6 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)	38.097, 101.317, 102.412
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Single Domain Camelid Nanobody VHH A2.3 Mass: 14351.988 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21 (bacteria)
#2: Protein/peptide	Microcystin-LR Type: Oligopeptide / Class: Toxin / Mass: 1016.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Microcystin-LR (MCLR) bound form
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.51 Å³/Da / Density % sol: 50.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 25% w/v PEG MME 3350, 200 mM ammonium sulfate, 100 mM HEPES

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.35→36.01 Å / Num. obs: 17031 / % possible obs: 99.1 % / Redundancy: 5.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.046 / R_rim(I) all: 0.082 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.35→2.43 Å / R_merge(I) obs: 0.997 / Num. unique obs: 1635 / R_pim(I) all: 0.68

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→35.685 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.919 / SU B: 12.994 / SU ML: 0.287 / Cross valid method: FREE R-VALUE / ESU R: 0.523 / ESU R Free: 0.296
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2801	847	4.985 %	0.05
R_work	0.2357	16143	-	-
all	0.238	-	-	-
obs	-	16990	98.693 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 60.214 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.013 Å²	-0 Å²	-0 Å²
2-	-	0.125 Å²	-0 Å²
3-	-	-	-0.138 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→35.685 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2768	0	213	142	3123

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	3037
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	2824
X-RAY DIFFRACTION	r_angle_refined_deg	1.92	1.742	4098
X-RAY DIFFRACTION	r_angle_other_deg	0.657	1.671	6433
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.415	5	354
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.127	5	27
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.555	10	460
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.529	10	135
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	432
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3714
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	840
X-RAY DIFFRACTION	r_nbd_refined	0.278	0.2	767
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.242	0.2	2930
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	1427
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	1836
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.275	0.2	154
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.188	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.147	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.22	0.2	7
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.01	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	7.2	5.916	1428
X-RAY DIFFRACTION	r_mcbond_other	7.198	5.917	1429
X-RAY DIFFRACTION	r_mcangle_it	9.66	10.592	1781
X-RAY DIFFRACTION	r_mcangle_other	9.659	10.595	1781
X-RAY DIFFRACTION	r_scbond_it	7.561	6.575	1609
X-RAY DIFFRACTION	r_scbond_other	7.559	6.574	1610
X-RAY DIFFRACTION	r_scangle_it	11.001	11.825	2317
X-RAY DIFFRACTION	r_scangle_other	10.999	11.823	2318
X-RAY DIFFRACTION	r_lrange_it	17.119	63.684	3540
X-RAY DIFFRACTION	r_lrange_other	17.115	63.685	3536

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.35-2.411	0.455	73	0.425	1155	0.427	1248	0.845	0.868	98.3974	0.411
2.411-2.477	0.461	58	0.414	1138	0.417	1197	0.86	0.887	99.9165	0.388
2.477-2.548	0.341	49	0.388	1136	0.386	1201	0.919	0.903	98.6678	0.355
2.548-2.626	0.371	62	0.331	1057	0.333	1119	0.886	0.932	100	0.294
2.626-2.712	0.371	61	0.28	1069	0.285	1133	0.918	0.954	99.7352	0.239
2.712-2.806	0.291	46	0.26	1006	0.261	1060	0.947	0.958	99.2453	0.223
2.806-2.911	0.35	42	0.252	1019	0.256	1065	0.932	0.961	99.6244	0.215
2.911-3.029	0.36	46	0.242	928	0.246	983	0.913	0.963	99.0844	0.209
3.029-3.163	0.353	34	0.261	872	0.265	981	0.896	0.956	92.3547	0.233
3.163-3.316	0.346	50	0.266	854	0.27	916	0.922	0.96	98.69	0.239
3.316-3.494	0.327	53	0.247	843	0.252	899	0.923	0.97	99.6663	0.233
3.494-3.704	0.195	39	0.237	793	0.235	833	0.973	0.975	99.88	0.23
3.704-3.956	0.274	37	0.223	749	0.225	791	0.956	0.976	99.3679	0.218
3.956-4.269	0.252	50	0.206	716	0.209	767	0.959	0.976	99.8696	0.205
4.269-4.67	0.184	33	0.171	643	0.171	678	0.976	0.982	99.705	0.175
4.67-5.21	0.262	31	0.18	592	0.185	627	0.965	0.982	99.362	0.185
5.21-5.995	0.241	26	0.204	515	0.206	567	0.972	0.977	95.4145	0.201
5.995-7.29	0.287	21	0.221	450	0.224	492	0.933	0.972	95.7317	0.214
7.29-10.102	0.295	25	0.2	369	0.206	395	0.941	0.974	99.7468	0.212
10.102-35.685	0.161	11	0.248	239	0.244	256	0.988	0.96	97.6562	0.266

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