8f5k

Azurin from Pseudomonas aeruginosa, Y72F/Y108F/F110A mutant

Method: X-RAY DIFFRACTION Dmax: 76.3 Å Quality: GOOD

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

Azurin

Pseudomonas aeruginosa

UniProt P00282

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–148 Mutation:Y72F,Y108F,F110A CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;22-25 % (w/v) PEG 3350, 0.1 M Hepes, pH 7.0, 0.2 M sodium formate Resolution 1.25 Å R-free 0.179
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–148 Mutation:Y72F,Y108F,F110A CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;22-25 % (w/v) PEG 3350, 0.1 M Hepes, pH 7.0, 0.2 M sodium formate Resolution 1.25 Å R-free 0.179
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–148 Mutation:Y72F,Y108F,F110A CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;22-25 % (w/v) PEG 3350, 0.1 M Hepes, pH 7.0, 0.2 M sodium formate Resolution 1.25 Å R-free 0.179
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–148 Mutation:Y72F,Y108F,F110A CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;22-25 % (w/v) PEG 3350, 0.1 M Hepes, pH 7.0, 0.2 M sodium formate Resolution 1.25 Å R-free 0.179

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.

110 other PDB entries and 267 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AZUR_PSEAE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–148; UniProt 1–148 Author chain B; PDBConstruct 1–148; UniProt 1–148 Author chain C; PDBConstruct 1–148; UniProt 1–148 Author chain D; PDBConstruct 1–148; UniProt 1–148

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 8f5k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8f5k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8f5k
Deposition date deposition_date2022-11-14
Structure title titleAzurin from Pseudomonas aeruginosa, Y72F/Y108F/F110A mutant
Keywords keywordscopper protein, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.05
Radius of gyration Rg (electron density) rg_electron22.18
Forward intensity I(0) i053608200.00
Molecular weight molecular_weight54926.0 kDa
Excluded volume excluded_volume67858 ų
Envelope volume envelope_volume80145 ų
Hydration-shell volume shell_volume29027 ų
Envelope diameter envelope_diameter77.5
Shell Rg shell_rg30.05
Envelope Rg envelope_rg22.44
Shape Rg shape_rg22.19
Total Rg total_rg23.01
Total atoms total_atoms3822
Residues n_residues505
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 dmax76.3
Rg (real space) rg_real22.89
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real5.3610e+07
I(0) uncertainty (real space) i0_real_error7.4680e+05
Rg (reciprocal space) rg_reciprocal22.93
I(0) (reciprocal space) i0_reciprocal53610000.0000
Solution quality estimate total_estimate0.8735
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.3
Skewness Skewness skewness0.143
Kurtosis Kurtosis kurtosis-0.364
Angular range angular_range— – 0.3450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11920000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.994

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)