5f0w

Crystal structure of human copper homeostatic proteins atox1

Method: X-RAY DIFFRACTION Dmax: 86.0 Å Quality: GOOD

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

Copper transport protein ATOX1

Homo sapiens

UniProt O00244

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 1–68 Not recorded AG SILVER ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350 Resolution 2.70 Å R-free 0.289
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–68 Not recorded AG SILVER ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350 Resolution 2.70 Å R-free 0.289
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–68 Not recorded AG SILVER ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350 Resolution 2.70 Å R-free 0.289
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–68 Not recorded AG SILVER ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M tri-sodium citrate, 20 % (W/V) PEG 3350 Resolution 2.70 Å R-free 0.289

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.

16 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ATOX1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–68; UniProt 1–68 Author chain B; PDBConstruct 1–68; UniProt 1–68 Author chain C; PDBConstruct 1–68; UniProt 1–68 Author chain D; PDBConstruct 1–68; UniProt 1–68

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 5f0w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5f0w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5f0w
Deposition date deposition_date2015-11-28
Structure title titleCrystal structure of human copper homeostatic proteins atox1
Keywords keywordscopper, homeostatic, 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_guinier24.66
Radius of gyration Rg (electron density) rg_electron24.68
Forward intensity I(0) i017460800.00
Molecular weight molecular_weight30470.0 kDa
Excluded volume excluded_volume37453 ų
Envelope volume envelope_volume47840 ų
Hydration-shell volume shell_volume17895 ų
Envelope diameter envelope_diameter88.5
Shell Rg shell_rg29.23
Envelope Rg envelope_rg24.63
Shape Rg shape_rg24.82
Total Rg total_rg24.81
Total atoms total_atoms2064
Residues n_residues272
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 dmax86.0
Rg (real space) rg_real24.89
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real1.7460e+07
I(0) uncertainty (real space) i0_real_error2.7850e+05
Rg (reciprocal space) rg_reciprocal24.84
I(0) (reciprocal space) i0_reciprocal17460000.0000
Solution quality estimate total_estimate0.8183
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.5
Skewness Skewness skewness0.446
Kurtosis Kurtosis kurtosis-0.356
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1597000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.539; Smooth: 0.806

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5f0wa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain
Domain ID domain_idd5f0wb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain
Domain ID domain_idd5f0wc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain
Domain ID domain_idd5f0wd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.17 — HMA, heavy metal-associated domain
Family Family familyd.58.17.1 — HMA, heavy metal-associated domain

CATH v4.4 (4 domains)

Domain ID domain_id5f0wA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100
Domain ID domain_id5f0wB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100
Domain ID domain_id5f0wC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100
Domain ID domain_id5f0wD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily100

8. Citations (1)

9. Files and Curves (10)