PDB-9fmy: X-ray structure of the adduct of bis(maltolato)oxidovanadium(IV) ...

ID or keywords:

Entry

Database: PDB / ID: 9fmy

Title

X-ray structure of the adduct of bis(maltolato)oxidovanadium(IV) with lysozyme upon the breakage of the maltolate ring

Components

Lysozyme C

Keywords

HYDROLASE / lysozyme / vanadium-based drug / protein metalation

Function / homology

Function and homology information

lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.09 Å

Authors

Paolillo, M. / Ferraro, G. / Merlino, A.

Funding support

Italy, 1items

Citation

Journal: Inorg Chem Front / Year: 2025
Title: Unexpected in crystallo reactivity of the potential drug bis (maltolato) oxidovanadium (IV) with lysozyme
Authors: Paolillo, M. / Ferraro, G. / Cipollone, I. / Garribba, E. / Monti, M. / Merlino, A.

History

Deposition	Jun 7, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fmy.cif.gz	77.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9fmy.ent.gz		Display	PDB format
PDBx/mmJSON format	9fmy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9fmy_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	9fmy_full_validation.pdf.gz	1.5 MB	Display
Data in XML	9fmy_validation.xml.gz	11.9 KB	Display
Data in CIF	9fmy_validation.cif.gz	16.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fm/9fmy ftp://data.pdbj.org/pub/pdb/validation_reports/fm/9fmy	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	#9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

AAA: Lysozyme C

hetero molecules

15.2 kDa, 1 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)	78.110, 78.110, 37.210
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	AAA-302- HOH
2	1	AAA-324- HOH
3	1	AAA-338- HOH
4	1	AAA-369- HOH
5	1	AAA-411- HOH
6	1	AAA-455- HOH
7	1	AAA-466- HOH

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Protein , 1 types, 1 molecules AAA

#1: Protein	Lysozyme C Mass: 14201.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK77, lysozyme

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Non-polymers , 6 types, 185 molecules

#2: Chemical	ChemComp-A1IE3 / bis(maltolato)oxidovanadium(IV) Mass: 541.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₁₉N₂O₁₄V₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-VVB / bis(oxidanyl)vanadium Mass: 84.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₂O₂V / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-A1IE4 / pentakis(oxidanyl)-oxidanylidene-vanadium Mass: 151.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₅O₆V / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / 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 Å³/Da / Density % sol: 38.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0

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Data collection

Diffraction	Mean temperature: 100 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: Jul 27, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.09→55.232 Å / Num. obs: 48619 / % possible obs: 99.9 % / Redundancy: 22.9 % / CC_1/2: 0.999 / Net I/σ(I): 29
Reflection shell	Resolution: 1.09→1.11 Å / Num. unique obs: 2359 / CC_1/2: 0.822

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.09→55.232 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.975 / SU B: 0.741 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.028
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1516	2489	5.22 %
R_work	0.1292	45192	-
all	0.13	-	-
obs	-	47681	98.255 %

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: 19.108 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.193 Å²	-0 Å²	-0 Å²
2-	-	0.193 Å²	-0 Å²
3-	-	-	-0.387 Å²

Refinement step

Cycle: LAST / Resolution: 1.09→55.232 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1024	0	18	176	1218

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.014	1111
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.014	986
X-RAY DIFFRACTION	r_angle_refined_deg	2.645	1.685	1515
X-RAY DIFFRACTION	r_angle_other_deg	1.795	1.594	2249
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.758	5	136
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.265	20.152	66
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.208	15	177
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.739	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.154	0.2	136
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.02	1311
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	300
X-RAY DIFFRACTION	r_nbd_refined	0.28	0.2	280
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.203	0.2	926
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	554
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.093	0.2	513
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.311	0.2	104
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.017	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.136	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.279	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.24	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.376	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	4.857	1.566	535
X-RAY DIFFRACTION	r_mcbond_other	4.161	1.552	534
X-RAY DIFFRACTION	r_mcangle_it	5.007	2.343	674
X-RAY DIFFRACTION	r_mcangle_other	5.069	2.363	675
X-RAY DIFFRACTION	r_scbond_it	4.27	1.98	575
X-RAY DIFFRACTION	r_scbond_other	4.346	1.974	566
X-RAY DIFFRACTION	r_scangle_it	5.029	2.842	841
X-RAY DIFFRACTION	r_scangle_other	5.021	2.823	833
X-RAY DIFFRACTION	r_lrange_it	5.014	20.901	1405
X-RAY DIFFRACTION	r_lrange_other	4.8	19.906	1350
X-RAY DIFFRACTION	r_rigid_bond_restr	15.291	3	2095

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
1.09-1.118	0.25	161	0.244	2841	0.244	3504	0.941	0.945	85.6735	0.212
1.118-1.149	0.22	148	0.203	3016	0.204	3447	0.952	0.962	91.79	0.171
1.149-1.182	0.197	185	0.174	3113	0.176	3342	0.957	0.967	98.6834	0.137
1.182-1.219	0.181	180	0.158	3092	0.16	3272	0.968	0.971	100	0.119
1.219-1.259	0.148	152	0.137	3006	0.137	3158	0.976	0.978	100	0.103
1.259-1.303	0.157	165	0.126	2899	0.128	3064	0.976	0.981	100	0.098
1.303-1.352	0.122	139	0.112	2822	0.112	2962	0.984	0.983	99.9662	0.087
1.352-1.407	0.134	151	0.106	2687	0.107	2840	0.983	0.985	99.9296	0.084
1.407-1.47	0.114	155	0.095	2592	0.096	2747	0.985	0.987	100	0.08
1.47-1.541	0.121	135	0.086	2502	0.088	2637	0.985	0.988	100	0.075
1.541-1.624	0.113	140	0.09	2373	0.091	2514	0.985	0.988	99.9602	0.083
1.624-1.723	0.146	112	0.092	2242	0.094	2354	0.98	0.987	100	0.089
1.723-1.842	0.124	117	0.099	2132	0.1	2250	0.982	0.986	99.9556	0.1
1.842-1.989	0.14	120	0.111	1959	0.113	2080	0.978	0.983	99.9519	0.12
1.989-2.179	0.142	94	0.112	1851	0.114	1945	0.979	0.984	100	0.127
2.179-2.435	0.142	90	0.11	1668	0.111	1758	0.975	0.983	100	0.129
2.435-2.811	0.138	80	0.123	1490	0.123	1570	0.976	0.978	100	0.15
2.811-3.441	0.156	72	0.131	1281	0.133	1353	0.972	0.978	100	0.169
3.441-4.857	0.155	60	0.137	1011	0.138	1071	0.978	0.979	100	0.176
4.857-55.232	0.256	33	0.265	609	0.265	647	0.894	0.921	99.2272	0.318

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Protein , 1 types, 1 molecules AAA

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