6gyi

Azurin fom Pseudomonas aeruginosa treated with hydrosulfide

Method: X-RAY DIFFRACTION Dmax: 101.7 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 Not recorded CU COPPER (II) ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2 Resolution 1.60 Å R-free 0.243
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–148 Not recorded CU COPPER (II) ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2 Resolution 1.60 Å R-free 0.243
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 21–148 Not recorded CU COPPER (II) ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2 Resolution 1.60 Å R-free 0.243
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 21–148 Not recorded CU COPPER (II) ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;30% PEG 4000, 100 mM NaHEPES pH 6,5, 200 mM CaCl2, 10 mM Na2S. Cryoprotectant: 10% PEG 4000, 20% PEG 400, 100 mM NaHEPES pH 6,5, 200 mM CaCl2 Resolution 1.60 Å R-free 0.243

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 6gyi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gyi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6gyi
Deposition date deposition_date2018-06-29
Structure title titleAzurin fom Pseudomonas aeruginosa treated with hydrosulfide
Keywords keywordscopper protein, hydrosulfide sensor, 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_guinier28.94
Radius of gyration Rg (electron density) rg_electron28.65
Forward intensity I(0) i054501200.00
Molecular weight molecular_weight55556.0 kDa
Excluded volume excluded_volume68590 ų
Envelope volume envelope_volume86103 ų
Hydration-shell volume shell_volume27253 ų
Envelope diameter envelope_diameter101.9
Shell Rg shell_rg33.18
Envelope Rg envelope_rg28.57
Shape Rg shape_rg28.63
Total Rg total_rg29.17
Total atoms total_atoms3861
Residues n_residues509
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 dmax101.7
Rg (real space) rg_real29.17
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real5.4500e+07
I(0) uncertainty (real space) i0_real_error8.4460e+05
Rg (reciprocal space) rg_reciprocal29.07
I(0) (reciprocal space) i0_reciprocal54500000.0000
Solution quality estimate total_estimate0.8323
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.576
Kurtosis Kurtosis kurtosis-0.103
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8650000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.735; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.701; Smooth: 0.909

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd6gyia_
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_idd6gyib_
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_idd6gyic_
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_idd6gyid_
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_id6gyiA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id6gyiB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id6gyiC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id6gyiD00
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)