4wkx

Reversible S-Nitrosylation in an Engineered Mutant of Pseudomonas aeruginosa Azurin with Red Copper Site

Method: X-RAY DIFFRACTION Dmax: 72.2 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 21–148 Mutation:H66E, M141H CU COPPER (II) ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;25% PEG 4000, 100 mM LiNO3, 10 mM CuSO4 and 100 mM Tris Resolution 1.94 Å R-free 0.235
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–148 Mutation:H66E, M141H CU COPPER (II) ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;25% PEG 4000, 100 mM LiNO3, 10 mM CuSO4 and 100 mM Tris Resolution 1.94 Å R-free 0.235
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 21–148 Chain B; UniProt 21–148 Mutation:H66E, M141H CU COPPER (II) ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;25% PEG 4000, 100 mM LiNO3, 10 mM CuSO4 and 100 mM Tris Resolution 1.94 Å R-free 0.235

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 268 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

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 4wkx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4wkx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4wkx
Deposition date deposition_date2014-10-03
Structure title titleReversible S-Nitrosylation in an Engineered Mutant of Pseudomonas aeruginosa Azurin with Red Copper Site
Keywords keywordsprotein engineering, Red copper site, S-nitrosylation, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.84
Radius of gyration Rg (electron density) rg_electron21.07
Forward intensity I(0) i015315900.00
Molecular weight molecular_weight28378.0 kDa
Excluded volume excluded_volume34939 ų
Envelope volume envelope_volume42593 ų
Hydration-shell volume shell_volume17383 ų
Envelope diameter envelope_diameter71.4
Shell Rg shell_rg26.56
Envelope Rg envelope_rg21.03
Shape Rg shape_rg21.05
Total Rg total_rg21.84
Total atoms total_atoms1994
Residues n_residues256
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 dmax72.2
Rg (real space) rg_real21.85
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real1.5320e+07
I(0) uncertainty (real space) i0_real_error2.1440e+05
Rg (reciprocal space) rg_reciprocal21.85
I(0) (reciprocal space) i0_reciprocal15320000.0000
Solution quality estimate total_estimate0.8863
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.6
Skewness Skewness skewness0.282
Kurtosis Kurtosis kurtosis-0.593
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2784000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.889; Smooth: 0.947

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4wkxa_
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_idd4wkxb_
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 (2 domains)

Domain ID domain_id4wkxA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4wkxB00
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)