3fi6

apo-H49AFr with high content of Pd ions

Method: X-RAY DIFFRACTION Dmax: 67.4 Å Quality: REASONABLE

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

Ferritin light chain

Equus caballus

UniProt P02791

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 homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric(24) Consistent with protein copy count Chain A; UniProt 2–175 Mutation:H49A, L93P PD PALLADIUM ION × 192 CD CADMIUM ION × 24 SO4 SULFATE ION × 24 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.80 Å R-free 0.225

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.

138 other PDB entries and 138 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FRIL_HORSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–174; UniProt 2–175

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 3fi6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fi6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fi6
Deposition date deposition_date2008-12-11
Structure title titleapo-H49AFr with high content of Pd ions
Keywords keywordsIron storage, light chain apoferritin, Metal binding protein; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.55
Radius of gyration Rg (electron density) rg_electron18.45
Forward intensity I(0) i08809210.00
Molecular weight molecular_weight20331.0 kDa
Excluded volume excluded_volume24541 ų
Envelope volume envelope_volume28607 ų
Hydration-shell volume shell_volume14105 ų
Envelope diameter envelope_diameter70.3
Shell Rg shell_rg22.90
Envelope Rg envelope_rg18.74
Shape Rg shape_rg18.29
Total Rg total_rg19.53
Total atoms total_atoms1374
Residues n_residues172
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 dmax67.4
Rg (real space) rg_real19.66
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real8.8090e+06
I(0) uncertainty (real space) i0_real_error1.1040e+05
Rg (reciprocal space) rg_reciprocal19.64
I(0) (reciprocal space) i0_reciprocal8809000.0000
Solution quality estimate total_estimate0.5990
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.0
Skewness Skewness skewness0.449
Kurtosis Kurtosis kurtosis-0.327
Angular range angular_range— – 0.4050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha985000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 0.278; Positv: 1.000; Valcen: 0.807; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3fi6a_
Class classa — All alpha proteins
Fold Fold folda.25 — Ferritin-like
Superfamily Superfamily superfamilya.25.1 — Ferritin-like
Family Family familya.25.1.1 — Ferritin

CATH v4.4 (1 domains)

Domain ID domain_id3fi6A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1260 — Ferritin
Homologous superfamily homologous superfamily10 — Ferritin, core subunit, four-helix bundle

8. Citations (1)

9. Files and Curves (10)