2e2v

Substrate Schiff-base analogue of copper amine oxidase from Arthrobacter globiformis formed with benzylhydrazine

Method: X-RAY DIFFRACTION Dmax: 106.4 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 1–628 Chain B; UniProt 1–628 Non-standard monomer:Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:MICRODIALYSIS;pH 6.8;289 K;0.3mM benzylhydrazine for 12h and at 310K, 10mg/ml enzyme solution, 1.05M potassium tartrate, 25mM HEPES at 289 K., pH 6.8, MICRODIALYSIS Resolution 1.80 Å R-free 0.252

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 1–628; UniProt 1–628 Author chain B; PDBConstruct 1–628; UniProt 1–628

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 2e2v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2e2v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2e2v
Deposition date deposition_date2006-11-17
Structure title titleSubstrate Schiff-base analogue of copper amine oxidase from Arthrobacter globiformis formed with benzylhydrazine
Keywords keywordsAmine oxidase, Topaquinone, TPQ, Benzylhydrazine, Substrate Schiff base, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.51
Radius of gyration Rg (electron density) rg_electron31.65
Forward intensity I(0) i0302059000.00
Molecular weight molecular_weight137920.0 kDa
Excluded volume excluded_volume171520 ų
Envelope volume envelope_volume202270 ų
Hydration-shell volume shell_volume51539 ų
Envelope diameter envelope_diameter111.7
Shell Rg shell_rg40.04
Envelope Rg envelope_rg31.78
Shape Rg shape_rg31.62
Total Rg total_rg32.35
Total atoms total_atoms9754
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 dmax106.4
Rg (real space) rg_real32.43
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real3.0210e+08
I(0) uncertainty (real space) i0_real_error4.6800e+06
Rg (reciprocal space) rg_reciprocal32.47
I(0) (reciprocal space) i0_reciprocal302100000.0000
Solution quality estimate total_estimate0.8759
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.1
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.236
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha95470000.0000
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: 0.873

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_idd2e2va1
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_idd2e2va2
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_idd2e2va3
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_idd2e2vb1
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_idd2e2vb2
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_idd2e2vb3
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_id2e2vA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2e2vA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2e2vA03
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_id2e2vB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2e2vB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2e2vB03
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)