4jkn

Mercury Metallated Pseudomonas aeruginosa Azurin at 1.54 A

Method: X-RAY DIFFRACTION Dmax: 75.4 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 HG MERCURY (II) ION × 2 NO3 NITRATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;298 K;3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 3 fold excess Mercury Chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.54 Å R-free 0.239
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 HG MERCURY (II) ION × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;298 K;3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 3 fold excess Mercury Chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.54 Å R-free 0.239
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 HG MERCURY (II) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;298 K;3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 3 fold excess Mercury Chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.54 Å R-free 0.239
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 HG MERCURY (II) ION × 1 NO3 NITRATE ION × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.5;298 K;3.2 M ammonium sulfate, 0.5 M lithium nitrate, 50 mM sodium acetate, pH 5.5, soaked with 3 fold excess Mercury Chloride , VAPOR DIFFUSION, SITTING DROP, temperature 298K Resolution 1.54 Å R-free 0.239

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 4jkn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4jkn
Deposition date deposition_date2013-03-10
Structure title titleMercury Metallated Pseudomonas aeruginosa Azurin at 1.54 A
Keywords keywordsElectron Transport, Mercury metallation; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.26
Radius of gyration Rg (electron density) rg_electron22.49
Forward intensity I(0) i062565800.00
Molecular weight molecular_weight57304.0 kDa
Excluded volume excluded_volume69567 ų
Envelope volume envelope_volume82573 ų
Hydration-shell volume shell_volume29476 ų
Envelope diameter envelope_diameter82.2
Shell Rg shell_rg30.69
Envelope Rg envelope_rg22.88
Shape Rg shape_rg22.56
Total Rg total_rg23.15
Total atoms total_atoms7743
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 dmax75.4
Rg (real space) rg_real23.13
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real6.2570e+07
I(0) uncertainty (real space) i0_real_error9.7260e+05
Rg (reciprocal space) rg_reciprocal23.16
I(0) (reciprocal space) i0_reciprocal62570000.0000
Solution quality estimate total_estimate0.8063
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.1
Skewness Skewness skewness0.187
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.3400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9872000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4jkna_
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_idd4jknb_
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_idd4jknc_
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_idd4jknd_
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_id4jknA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4jknB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4jknC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id4jknD00
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)