PDB-9i8l: X-ray structure of a polyoxidovanadate/lysozyme adduct obtained w...

ID or keywords:

Entry

Database: PDB / ID: 9i8l

Title

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] at 310 K

Components

Lysozyme C

Keywords

HYDROLASE / POV / protein / vanadium / polyoxidovanadate / metal protein interaction

Function / homology

Function and homology information

Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.831 Å

Authors

Tito, G. / Ferraro, G. / Merlino, A.

Funding support

Italy, 2items

Organization	Grant number	Country
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)	2022JMFC3X	Italy
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)	2022APCTNA	Italy

Citation

Journal: Chemistry / Year: 2025
Title: Formation of Mixed-Valence Cage-Like Polyoxidovanadates at 37°C Upon Reaction of V IV O(acetylacetonato) 2 With Lysozyme.
Authors: Tito, G. / Ferraro, G. / Garribba, E. / Merlino, A.

History

Deposition	Feb 5, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 21, 2025	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Jun 18, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9i8l.cif.gz	48.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9i8l.ent.gz		Display	PDB format
PDBx/mmJSON format	9i8l.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/i8/9i8l ftp://data.pdbj.org/pub/pdb/validation_reports/i8/9i8l	HTTPS FTP

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Related structure data

Similar structure data	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	#21 - Sep 2001 Antibodies similarity (3) #136 - Apr 2011 Nanobodies similarity (3) #222 - Jun 2018 Proteins and Nanoparticles similarity (3) #9 - Sep 2000 Lysozyme similarity (3) #142 - Oct 2011 PDB Pioneers similarity (3)

Deposited unit

A: Lysozyme C

hetero molecules

17.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Lysozyme C

hetero molecules

A: Lysozyme C

hetero molecules

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

Unit cell

Length a, b, c (Å)	80.860, 80.860, 36.830
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-203- A1ICR
2	1	A-305- HOH
3	1	A-318- HOH
4	1	A-333- HOH
5	1	A-334- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 61 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-A1ICR / Polyoxidovanadate complex / VUF-6884 Mass: 1834.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₅₁V₂₀ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-A1H8D / Polyoxidovanadate complex Mass: 1292.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₃₃V₁₅ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.1 Å³/Da / Density % sol: 41.44 %
Crystal grow	Temperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1,1 M sodium chloride and 0,1 M sodium acetate buffer pH 4.0

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Data collection

Diffraction	Mean temperature: 310 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.83→57.177 Å / Num. obs: 10096 / % possible obs: 90 % / Redundancy: 8.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.116 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.83→1.86 Å / Redundancy: 8.8 % / R_merge(I) obs: 6.402 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 550 / CC_1/2: 0.369 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.831→57.177 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.912 / SU B: 5.807 / SU ML: 0.169 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.216
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2838	428	4.902 %
R_work	0.2001	8304	-
all	0.205	-	-
obs	-	8732	77.721 %

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: 40.129 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.389 Å²	0 Å²	-0 Å²
2-	-	-0.389 Å²	0 Å²
3-	-	-	0.779 Å²

Refinement step

Cycle: LAST / Resolution: 1.831→57.177 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1001	0	86	57	1144

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	1165
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	896
X-RAY DIFFRACTION	r_angle_refined_deg	1.847	1.567	1632
X-RAY DIFFRACTION	r_angle_other_deg	0.469	1.564	2092
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.519	5	133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.367	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.382	10	171
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.956	10	53
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	148
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1263
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	229
X-RAY DIFFRACTION	r_nbd_refined	0.267	0.2	264
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	826
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	504
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	523
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.425	0.2	45
X-RAY DIFFRACTION	r_metal_ion_refined	0.09	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.312	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.209	0.2	17
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.285	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.159	3.951	529
X-RAY DIFFRACTION	r_mcbond_other	3.118	3.951	529
X-RAY DIFFRACTION	r_mcangle_it	4.091	5.915	663
X-RAY DIFFRACTION	r_mcangle_other	4.092	5.923	664
X-RAY DIFFRACTION	r_scbond_it	4.563	5.075	636
X-RAY DIFFRACTION	r_scbond_other	3.955	4.422	522
X-RAY DIFFRACTION	r_scangle_it	5.651	7.559	947
X-RAY DIFFRACTION	r_scangle_other	5.848	6.465	762
X-RAY DIFFRACTION	r_lrange_it	9.008	73.95	1303
X-RAY DIFFRACTION	r_lrange_other	8.892	72.481	1290

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
1.831-1.879	0.375	2	0.354	51	0.356	807	0.964	0.902	6.5675	0.348
1.879-1.93	0.123	3	0.3	106	0.296	802	0.969	0.923	13.591	0.301
1.93-1.986	0.358	22	0.302	404	0.305	756	0.901	0.93	56.3492	0.302
1.986-2.047	0.35	31	0.285	591	0.288	751	0.908	0.938	82.8229	0.273
2.047-2.114	0.287	19	0.248	492	0.25	723	0.971	0.955	70.6777	0.233
2.114-2.188	0.281	33	0.268	644	0.269	710	0.947	0.948	95.3521	0.247
2.188-2.271	0.352	26	0.237	532	0.243	680	0.916	0.957	82.0588	0.204
2.271-2.364	0.326	27	0.24	618	0.244	646	0.95	0.956	99.8452	0.22
2.364-2.468	0.321	32	0.218	608	0.223	642	0.93	0.965	99.6885	0.191
2.468-2.589	0.282	28	0.208	564	0.211	593	0.948	0.969	99.8314	0.182
2.589-2.728	0.513	23	0.226	464	0.238	581	0.906	0.965	83.821	0.201
2.728-2.893	0.253	25	0.204	529	0.206	554	0.949	0.968	100	0.192
2.893-3.093	0.356	26	0.213	495	0.219	521	0.917	0.967	100	0.21
3.093-3.34	0.282	24	0.195	461	0.2	485	0.955	0.973	100	0.201
3.34-3.657	0.261	17	0.186	389	0.189	453	0.951	0.975	89.6247	0.202
3.657-4.087	0.195	16	0.175	324	0.176	419	0.981	0.978	81.1456	0.202
4.087-4.715	0.225	27	0.159	339	0.164	366	0.969	0.982	100	0.191
4.715-5.765	0.262	14	0.179	305	0.183	321	0.957	0.977	99.3769	0.216
5.765-8.112	0.252	19	0.183	239	0.187	258	0.956	0.975	100	0.231
8.112-57.177	0.365	14	0.192	149	0.205	164	0.901	0.971	99.3902	0.244

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