1sfd

oxidized form of amicyanin mutant P94F

Method: X-RAY DIFFRACTION Dmax: 71.1 Å Quality: REASONABLE

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 Mutation:P94F CU COPPER (II) ION × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;293 K;100 mM sodium citrate, 2.25 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K Resolution 0.99 Å R-free 0.147
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 27–131 Mutation:P94F CU COPPER (II) ION × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.6;293 K;100 mM sodium citrate, 2.25 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K Resolution 0.99 Å R-free 0.147

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 56 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 Author chain B; 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 1sfd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1sfd
Deposition date deposition_date2004-02-19
Structure title titleoxidized form of amicyanin mutant P94F
Keywords keywordsblue 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_guinier19.74
Radius of gyration Rg (electron density) rg_electron19.36
Forward intensity I(0) i010528800.00
Molecular weight molecular_weight23680.0 kDa
Excluded volume excluded_volume29356 ų
Envelope volume envelope_volume34283 ų
Hydration-shell volume shell_volume15644 ų
Envelope diameter envelope_diameter71.0
Shell Rg shell_rg24.31
Envelope Rg envelope_rg19.65
Shape Rg shape_rg19.42
Total Rg total_rg19.91
Total atoms total_atoms1649
Residues n_residues210
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 dmax71.1
Rg (real space) rg_real19.86
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real1.0530e+07
I(0) uncertainty (real space) i0_real_error1.4530e+05
Rg (reciprocal space) rg_reciprocal19.84
I(0) (reciprocal space) i0_reciprocal10530000.0000
Solution quality estimate total_estimate0.6140
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0
Skewness Skewness skewness0.515
Kurtosis Kurtosis kurtosis-0.172
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2199000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.653; Stabil: 1.000; Sysdev: 0.424; Positv: 1.000; Valcen: 0.746; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1sfda_
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_idd1sfdb_
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_id1sfdA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id1sfdB00
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)