4p5s

Structure of reduced W45Y mutant of amicyanin

Method: X-RAY DIFFRACTION Dmax: 43.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Amicyanin

Paracoccus denitrificans

UniProt P22364

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 27–131 Fragment:UNP residues 27-131 Mutation:W45Y CU1 COPPER (I) ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;Initial crystals were obtained from Hampton research ammonium sulfate screen (HR2-211). Bigger crystals grown by macro-seeding using 3.2M Na/K phosphate solution. Resolution 1.02 Å R-free 0.150

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.

34 other PDB entries and 57 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMCY_PARDE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–105; UniProt 27–131

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 4p5s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4p5s
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id4p5s
Deposition date deposition_date2014-03-19
Structure title titleStructure of reduced W45Y mutant of amicyanin
Keywords keywordsType-I blue copper protein, Beta sandwich, 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_guinier13.79
Radius of gyration Rg (electron density) rg_electron12.47
Forward intensity I(0) i02715190.00
Molecular weight molecular_weight11527.0 kDa
Excluded volume excluded_volume14428 ų
Envelope volume envelope_volume15362 ų
Hydration-shell volume shell_volume10525 ų
Envelope diameter envelope_diameter42.2
Shell Rg shell_rg18.25
Envelope Rg envelope_rg12.74
Shape Rg shape_rg12.44
Total Rg total_rg13.86
Total atoms total_atoms806
Residues n_residues105
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 dmax43.8
Rg (real space) rg_real13.69
Rg uncertainty (real space) rg_real_error0.19
I(0) (real space) i0_real2.7150e+06
I(0) uncertainty (real space) i0_real_error2.7700e+04
Rg (reciprocal space) rg_reciprocal13.70
I(0) (reciprocal space) i0_reciprocal2715000.0000
Solution quality estimate total_estimate0.8942
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.7
Skewness Skewness skewness0.067
Kurtosis Kurtosis kurtosis-0.442
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha454600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4p5sa_
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 (1 domains)

Domain ID domain_id4p5sA00
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)