3in0

Crystal structure of the F114P/M121Q variant of Pseudomonas aeruginosa azurin in the Cu(II) state

Method: X-RAY DIFFRACTION Dmax: 86.5 Å Quality: EXCELLENT

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 21–148 Mutation:F114P, M121Q CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;PEG 8000, 0.08M NaOAc, 0.2M Lithium nitrate, 0.2M Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.35 Å R-free 0.286
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–148 Mutation:F114P, M121Q CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;PEG 8000, 0.08M NaOAc, 0.2M Lithium nitrate, 0.2M Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.35 Å R-free 0.286
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 21–148 Mutation:F114P, M121Q CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;PEG 8000, 0.08M NaOAc, 0.2M Lithium nitrate, 0.2M Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.35 Å R-free 0.286
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 21–148 Mutation:F114P, M121Q CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;277 K;PEG 8000, 0.08M NaOAc, 0.2M Lithium nitrate, 0.2M Calcium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.35 Å R-free 0.286

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 1–128; UniProt 21–148 Author chain B; PDBConstruct 1–128; UniProt 21–148 Author chain C; PDBConstruct 1–128; UniProt 21–148 Author chain D; PDBConstruct 1–128; UniProt 21–148

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 3in0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3in0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3in0
Deposition date deposition_date2009-08-11
Structure title titleCrystal structure of the F114P/M121Q variant of Pseudomonas aeruginosa azurin in the Cu(II) state
Keywords keywords;CUPREDOXIN, AZURIN, GREEK KEY, BETA BARREL, ELECTRON TRANSFER, Copper, Disulfide bond, Electron transport, Metal-binding, Periplasm, Transport ;; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.43
Radius of gyration Rg (electron density) rg_electron25.70
Forward intensity I(0) i055664500.00
Molecular weight molecular_weight55745.0 kDa
Excluded volume excluded_volume68776 ų
Envelope volume envelope_volume85016 ų
Hydration-shell volume shell_volume28244 ų
Envelope diameter envelope_diameter87.7
Shell Rg shell_rg32.38
Envelope Rg envelope_rg25.54
Shape Rg shape_rg25.68
Total Rg total_rg26.47
Total atoms total_atoms3884
Residues n_residues512
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 dmax86.5
Rg (real space) rg_real26.38
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real5.5660e+07
I(0) uncertainty (real space) i0_real_error7.7560e+05
Rg (reciprocal space) rg_reciprocal26.40
I(0) (reciprocal space) i0_reciprocal55670000.0000
Solution quality estimate total_estimate0.9013
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.3
Skewness Skewness skewness0.242
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7346000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.989

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3in0a_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd3in0b_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd3in0c_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd3in0d_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like

CATH v4.4 (4 domains)

Domain ID domain_id3in0A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3in0B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3in0C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3in0D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins

8. Citations (1)

9. Files and Curves (10)