4kob

Investigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95I)

Method: X-RAY DIFFRACTION Dmax: 77.3 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 Fragment:UNP residues 21-148 Mutation:V31I/V95I CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.87 Å R-free 0.226
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 21–148 Fragment:UNP residues 21-148 Mutation:V31I/V95I CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.87 Å R-free 0.226
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 21–148 Fragment:UNP residues 21-148 Mutation:V31I/V95I CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.87 Å R-free 0.226
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 21–148 Fragment:UNP residues 21-148 Mutation:V31I/V95I CU COPPER (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;293 K;100 mM Tris-HCl, 100 mM lithium nitrate, 10 mM copper sulfate, 30% PEG4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.87 Å R-free 0.226

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 4kob

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4kob
Deposition date deposition_date2013-05-11
Structure title titleInvestigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/V95I)
Keywords keywordscupredoxin fold, computational protein design, copper binding, 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_guinier26.67
Radius of gyration Rg (electron density) rg_electron25.58
Forward intensity I(0) i055746900.00
Molecular weight molecular_weight56070.0 kDa
Excluded volume excluded_volume69349 ų
Envelope volume envelope_volume87535 ų
Hydration-shell volume shell_volume28454 ų
Envelope diameter envelope_diameter83.3
Shell Rg shell_rg32.72
Envelope Rg envelope_rg25.00
Shape Rg shape_rg25.54
Total Rg total_rg26.49
Total atoms total_atoms3904
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 dmax77.3
Rg (real space) rg_real26.45
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real5.5750e+07
I(0) uncertainty (real space) i0_real_error6.8190e+05
Rg (reciprocal space) rg_reciprocal26.52
I(0) (reciprocal space) i0_reciprocal55750000.0000
Solution quality estimate total_estimate0.9074
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.6
Skewness Skewness skewness-0.082
Kurtosis Kurtosis kurtosis-0.675
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8592000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.973

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_idd4koba_
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_idd4kobb_
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_idd4kobc_
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_idd4kobd_
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_id4kobA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4kobB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4kobC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4kobD00
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)