2wof

EDTA treated E. coli copper amine oxidase

Method: X-RAY DIFFRACTION Dmax: 105.1 Å Quality: GOOD

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

PRIMARY AMINE OXIDASE

ESCHERICHIA COLI

UniProt P46883

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 31–757 Chain B; UniProt 31–757 Non-standard monomer:Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 NA SODIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.25 Å R-free 0.220

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 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMO_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–727; UniProt 31–757 Author chain B; PDBConstruct 1–727; UniProt 31–757

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 2wof

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2wof
Deposition date deposition_date2009-07-23
Structure title titleEDTA treated E. coli copper amine oxidase
Keywords keywordsOXIDOREDUCTASE, AMINE OXIDATION, TPQ, METAL-BINDING; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.88
Radius of gyration Rg (electron density) rg_electron33.19
Forward intensity I(0) i0393534000.00
Molecular weight molecular_weight161060.0 kDa
Excluded volume excluded_volume201620 ų
Envelope volume envelope_volume243370 ų
Hydration-shell volume shell_volume58059 ų
Envelope diameter envelope_diameter114.8
Shell Rg shell_rg42.13
Envelope Rg envelope_rg33.40
Shape Rg shape_rg33.16
Total Rg total_rg33.91
Total atoms total_atoms11355
Residues n_residues1438
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 dmax105.1
Rg (real space) rg_real33.72
Rg uncertainty (real space) rg_real_error0.72
I(0) (real space) i0_real3.9350e+08
I(0) uncertainty (real space) i0_real_error6.1320e+06
Rg (reciprocal space) rg_reciprocal33.82
I(0) (reciprocal space) i0_reciprocal393600000.0000
Solution quality estimate total_estimate0.8972
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.5
Skewness Skewness skewness0.181
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha112000000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2wofa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamilyd.82.1 — Copper amine oxidase, domain N
Family Family familyd.82.1.1 — Copper amine oxidase, domain N
Domain ID domain_idd2wofa2
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_idd2wofa3
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_idd2wofa4
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_idd2wofb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.82 — N domain of copper amine oxidase-like
Superfamily Superfamily superfamilyd.82.1 — Copper amine oxidase, domain N
Family Family familyd.82.1.1 — Copper amine oxidase, domain N
Domain ID domain_idd2wofb2
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_idd2wofb3
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_idd2wofb4
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

CATH v4.4 (8 domains)

Domain ID domain_id2wofA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Copper amine oxidase-like, N-terminal domain
Domain ID domain_id2wofA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2wofA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2wofA04
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_id2wofB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology457 — Copper Amine Oxidase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Copper amine oxidase-like, N-terminal domain
Domain ID domain_id2wofB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2wofB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id2wofB04
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)