5syd

Circularly permutated azurin (cpAz) based on P. aeruginosa azurin sequence

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD

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

Azurin, chimeric construct

Pseudomonas aeruginosa

UniProt B3EWN9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–38 Fragment:unp residues 63-148; 1-38 CU COPPER (II) ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, with 300 uL well buffer in the crystallization tray. Resolution 2.40 Å R-free 0.251
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–38 Fragment:unp residues 63-148; 1-38 CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, with 300 uL well buffer in the crystallization tray. Resolution 2.40 Å R-free 0.251

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name AZUR_PSEAI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 94–131; UniProt 1–38 Author chain B; PDBConstruct 94–131; UniProt 1–38

Azurin, chimeric construct

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 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 63–148 Fragment:unp residues 63-148; 1-38 CU COPPER (II) ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, with 300 uL well buffer in the crystallization tray. Resolution 2.40 Å R-free 0.251
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 63–148 Fragment:unp residues 63-148; 1-38 CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277 K;2 uL of 5 mM protein was mixed with equal amount of well buffer (0.1 M Tris, 0.1 M LiNO 3, 0.01 M CUSO 4 with 35% polyethylene glycol 10000), and crystalized using the hanging drop method, with 300 uL well buffer in the crystallization tray. Resolution 2.40 Å R-free 0.251

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 269 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 3–88; UniProt 63–148 Author chain B; PDBConstruct 3–88; UniProt 63–148

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 5syd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5syd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5syd
Deposition date deposition_date2016-08-10
Structure title titleCircularly permutated azurin (cpAz) based on P. aeruginosa azurin sequence
Keywords keywordscupredoxin, engineered, greek-key beta barrel, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.66
Radius of gyration Rg (electron density) rg_electron21.31
Forward intensity I(0) i015355300.00
Molecular weight molecular_weight28241.0 kDa
Excluded volume excluded_volume34727 ų
Envelope volume envelope_volume42196 ų
Hydration-shell volume shell_volume17557 ų
Envelope diameter envelope_diameter78.8
Shell Rg shell_rg26.59
Envelope Rg envelope_rg21.69
Shape Rg shape_rg21.32
Total Rg total_rg21.98
Total atoms total_atoms1957
Residues n_residues261
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 dmax78.8
Rg (real space) rg_real21.84
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real1.5360e+07
I(0) uncertainty (real space) i0_real_error2.3730e+05
Rg (reciprocal space) rg_reciprocal21.81
I(0) (reciprocal space) i0_reciprocal15360000.0000
Solution quality estimate total_estimate0.8060
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.7
Skewness Skewness skewness0.557
Kurtosis Kurtosis kurtosis-0.142
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3818000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.616; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.628; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)