9ex0

X-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure A)

Method: X-RAY DIFFRACTION Dmax: 50.2 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysozyme C

OrganismNot specified

UniProt P00698

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 19–147 Not recorded CL CHLORIDE ION × 6 NA SODIUM ION × 2 A1ICR Polyoxidovanadate complex × 2 VO4 VANADATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;293 K;1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 Resolution 1.45 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

1320 other PDB entries and 1450 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LYSC_CHICK
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–129; UniProt 19–147

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9ex0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ex0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ex0
Deposition date deposition_date2024-04-05
Structure title titleX-ray structure of a polyoxidovanadate/lysozyme adduct obtained when the protein is treated with [VIVO(acac)2] in 1.1 M NaCl, 0.1 M sodium acetate at pH 4.0 (Structure A)
Keywords keywordslysozyme, vanadium, acetoacetonate, POV, cluster, mixed valence, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.32
Radius of gyration Rg (electron density) rg_electron14.03
Forward intensity I(0) i06042180.00
Molecular weight molecular_weight15491.0 kDa
Excluded volume excluded_volume18238 ų
Envelope volume envelope_volume20110 ų
Hydration-shell volume shell_volume12279 ų
Envelope diameter envelope_diameter49.9
Shell Rg shell_rg19.70
Envelope Rg envelope_rg14.29
Shape Rg shape_rg13.97
Total Rg total_rg15.14
Total atoms total_atoms1046
Residues n_residues129
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax50.2
Rg (real space) rg_real15.22
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real6.0420e+06
I(0) uncertainty (real space) i0_real_error5.5180e+04
Rg (reciprocal space) rg_reciprocal15.23
I(0) (reciprocal space) i0_reciprocal6042000.0000
Solution quality estimate total_estimate0.8838
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.138
Kurtosis Kurtosis kurtosis-0.318
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha494000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)