1wmo

Crystal structure of topaquinone-containing amine oxidase activated by nickel ion

Method: X-RAY DIFFRACTION Dmax: 106.2 Å Quality: GOOD

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

Phenylethylamine oxidase

Arthrobacter globiformis

UniProt P46881

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–638 Chain B; UniProt 1–638 Non-standard monomer:Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 6.8;289 K;1.05M POTASSIUM SODIUM TARTRATE, 25mM HEPES, pH 6.8, MICRODIALYSIS, temperature 289K Resolution 1.80 Å R-free 0.266

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.

105 other PDB entries and 143 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAOX_ARTGO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–638; UniProt 1–638 Author chain B; PDBConstruct 1–638; UniProt 1–638

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 1wmo

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1wmo
Deposition date deposition_date2004-07-13
Structure title titleCrystal structure of topaquinone-containing amine oxidase activated by nickel ion
Keywords keywordsOXIDOREDUCTASE, COPPER, Amine Oxidase, TOPAQUINONE, TPQ, Nickel, Biogenesis; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.44
Radius of gyration Rg (electron density) rg_electron31.59
Forward intensity I(0) i0301465000.00
Molecular weight molecular_weight137710.0 kDa
Excluded volume excluded_volume171220 ų
Envelope volume envelope_volume201740 ų
Hydration-shell volume shell_volume51451 ų
Envelope diameter envelope_diameter113.3
Shell Rg shell_rg40.02
Envelope Rg envelope_rg31.75
Shape Rg shape_rg31.56
Total Rg total_rg32.29
Total atoms total_atoms9738
Residues n_residues1238
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 dmax106.2
Rg (real space) rg_real32.36
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real3.0150e+08
I(0) uncertainty (real space) i0_real_error4.8310e+06
Rg (reciprocal space) rg_reciprocal32.39
I(0) (reciprocal space) i0_reciprocal301500000.0000
Solution quality estimate total_estimate0.8760
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.0
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.235
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha91590000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.877

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1wmoa1
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
Family Family familyb.30.2.1 — Amine oxidase catalytic domain
Domain ID domain_idd1wmoa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1wmoa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1wmob1
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
Family Family familyb.30.2.1 — Amine oxidase catalytic domain
Domain ID domain_idd1wmob2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1wmob3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (6 domains)

Domain ID domain_id1wmoA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1wmoA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1wmoA03
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain
Domain ID domain_id1wmoB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1wmoB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1wmoB03
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain

8. Citations (1)

9. Files and Curves (10)