4ko5

Investigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/W48L/V95I/Y108F)

Method: X-RAY DIFFRACTION Dmax: 64.3 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 Fragment:UNP residues 21-148 Mutation:V31I/W48L/V95I/Y108F 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 1.79 Å R-free 0.240
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/W48L/V95I/Y108F 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 1.79 Å R-free 0.240

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 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 4ko5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ko5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ko5
Deposition date deposition_date2013-05-11
Structure title titleInvestigating the functional significance of the interlocked pair structural determinants in Pseudomonas aeruginosa azurin (V31I/W48L/V95I/Y108F)
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_guinier20.22
Radius of gyration Rg (electron density) rg_electron19.39
Forward intensity I(0) i014618700.00
Molecular weight molecular_weight27891.0 kDa
Excluded volume excluded_volume34525 ų
Envelope volume envelope_volume41125 ų
Hydration-shell volume shell_volume18050 ų
Envelope diameter envelope_diameter65.6
Shell Rg shell_rg25.13
Envelope Rg envelope_rg19.34
Shape Rg shape_rg19.39
Total Rg total_rg20.17
Total atoms total_atoms1940
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 dmax64.3
Rg (real space) rg_real20.15
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real1.4620e+07
I(0) uncertainty (real space) i0_real_error1.7250e+05
Rg (reciprocal space) rg_reciprocal20.16
I(0) (reciprocal space) i0_reciprocal14620000.0000
Solution quality estimate total_estimate0.8278
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.7
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.490
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2095000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ko5a_
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_idd4ko5b_
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_id4ko5A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4ko5B00
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)