1jvo

Azurin dimer, crosslinked via disulfide bridge

Method: X-RAY DIFFRACTION Dmax: 180.3 Å Quality: REASONABLE

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 21–148 Chain B; UniProt 21–148 Chain C; UniProt 21–148 Chain D; UniProt 21–148 Fragment:Azurin Mutation:N42C CU COPPER (II) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K, temperature 293.0K Resolution 2.75 Å R-free 0.289
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 21–148 Chain F; UniProt 21–148 Chain G; UniProt 21–148 Chain H; UniProt 21–148 Fragment:Azurin Mutation:N42C CU COPPER (II) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K, temperature 293.0K Resolution 2.75 Å R-free 0.289
3 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 21–148 Chain J; UniProt 21–148 Chain K; UniProt 21–148 Chain L; UniProt 21–148 Fragment:Azurin Mutation:N42C CU COPPER (II) ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;PEG 8000, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 293K, temperature 293.0K Resolution 2.75 Å R-free 0.289

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 Author chain C; PDBConstruct 1–128; UniProt 21–148 Author chain D; PDBConstruct 1–128; UniProt 21–148 Author chain E; PDBConstruct 1–128; UniProt 21–148 Author chain F; PDBConstruct 1–128; UniProt 21–148 Author chain G; PDBConstruct 1–128; UniProt 21–148 Author chain H; PDBConstruct 1–128; UniProt 21–148 Author chain I; PDBConstruct 1–128; UniProt 21–148 Author chain J; PDBConstruct 1–128; UniProt 21–148 Author chain K; PDBConstruct 1–128; UniProt 21–148 Author chain L; 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 1jvo

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jvo
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jvo
Deposition date deposition_date2001-08-30
Structure title titleAzurin dimer, crosslinked via disulfide bridge
Keywords keywordscupredoxin, electron transfer, covalent crosslink, 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_guinier59.05
Radius of gyration Rg (electron density) rg_electron60.15
Forward intensity I(0) i0445968000.00
Molecular weight molecular_weight167940.0 kDa
Excluded volume excluded_volume207420 ų
Envelope volume envelope_volume373940 ų
Hydration-shell volume shell_volume59739 ų
Envelope diameter envelope_diameter193.2
Shell Rg shell_rg49.88
Envelope Rg envelope_rg56.86
Shape Rg shape_rg60.14
Total Rg total_rg59.78
Total atoms total_atoms11676
Residues n_residues1536
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 dmax180.3
Rg (real space) rg_real59.64
Rg uncertainty (real space) rg_real_error1.61
I(0) (real space) i0_real4.4600e+08
I(0) uncertainty (real space) i0_real_error9.4220e+06
Rg (reciprocal space) rg_reciprocal58.50
I(0) (reciprocal space) i0_reciprocal445100000.0000
Solution quality estimate total_estimate0.6657
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks4
Primary peak position r_peak_primary73.5
Skewness Skewness skewness0.435
Kurtosis Kurtosis kurtosis-0.608
Angular range angular_range— – 0.1350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9930000.0000
Real-space data points n_real_points28
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.269; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1jvoa_
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_idd1jvob_
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_idd1jvoc_
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_idd1jvod_
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_idd1jvoe_
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_idd1jvof_
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_idd1jvog_
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_idd1jvoh_
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_idd1jvoi_
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_idd1jvoj_
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_idd1jvok_
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_idd1jvol_
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 (12 domains)

Domain ID domain_id1jvoA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1jvoL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins

8. Citations (2)

9. Files and Curves (10)