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6ezz

Crystal structure of Escherichia coli amine oxidase mutant E573Q

Method: X-RAY DIFFRACTION Dmax: 105.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Primary amine oxidase

Escherichia coli (strain K12)

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 Mutation：E573Q CU COPPER (II) ION × 2 CA CALCIUM ION × 2 GOL GLYCEROL × 9 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291.15 K；1.6 M Sodium citrate, 100mM HEPES pH 6-7 Resolution 1.80 Å R-free 0.197

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.

Other PDB Difference from Current Entry 6EZZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D6U CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE Deposited 1999-10-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 HY1 PHENYLACETALDEHYDE × 2 PEA 2-PHENYLETHYLAMINE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；291 K；SODIUM CITRATE, HEPES BUFFER, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Resolution 2.40 Å R-free 0.239
1D6Y CRYSTAL STRUCTURE OF E. COLI COPPER-CONTAINING AMINE OXIDASE ANAEROBICALLY REDUCED WITH BETA-PHENYLETHYLAMINE AND COMPLEXED WITH NITRIC OXIDE. Deposited 1999-10-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 HY1 PHENYLACETALDEHYDE × 2 NO NITRIC OXIDE × 2 PEA 2-PHENYLETHYLAMINE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；291 K；sodium citrate, HEPES buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Resolution 2.40 Å R-free 0.231
1D6Z CRYSTAL STRUCTURE OF THE AEROBICALLY FREEZE TRAPPED RATE-DETERMINING CATALYTIC INTERMEDIATE OF E. COLI COPPER-CONTAINING AMINE OXIDASE. Deposited 1999-10-16 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 HY1 PHENYLACETALDEHYDE × 2 PEO HYDROGEN PEROXIDE × 2 PEA 2-PHENYLETHYLAMINE × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；291 K；sodium citrate, HEPES buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Resolution 2.10 Å R-free 0.237
1DYU The active site base controls cofactor reactivity in Escherichia coli amine oxidase: X-ray crystallographic studies with mutational variants. Deposited 2000-02-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；1.2 M SODIUM CITRATE, 0.1 M HEPES PH 7.1
Resolution 2.04 Å R-free 0.237
1JRQ X-ray Structure Analysis of the Role of the Conserved Tyrosine-369 in Active Site of E. coli Amine Oxidase Deposited 2001-08-14 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Mutation：Y369F Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Y369F Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；SODIUM CITRATE, HEPES BUFFER, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.15 Å R-free 0.235
1LVN CRYSTAL STRUCTURE OF E. COLI AMINE OXIDASE COMPLEXED WITH TRANYLCYPROMINE Deposited 2002-05-28 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions Sitting drop；pH 7.2；291 K；1.3M SODIUM CITRATE, 0.1M HEPES BUFFER, pH 7.2, INHIBITOR SOAKING SOLUTION 10:1 RATIO OF RACEMIC TRANYLCYPROMINE TO ENZYME MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL SOAKED FOR 20 DAYS.CRYOPROTECTANT 20% GLYCEROL, 1.4M SODIUM CITRATE BUFFER, PH 7.2, pH 7.20, Sitting drop, temperature 291.0K
Resolution 2.40 Å R-free 0.229
1OAC CRYSTAL STRUCTURE OF A QUINOENZYME: COPPER AMINE OXIDASE OF ESCHERICHIA COLI AT 2 ANGSTROEMS RESOLUTION Deposited 1995-09-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1QAF THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA COLI AMINE OXIDASE : X-RAY CRYSTALLOGRAPHIC STUDIES WITH MUTATIONAL VARIANTS Deposited 1999-03-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–756（721 aa）
Chain B 36–756（721 aa）
Mutation：D383E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D383E Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；315 K；VAPOR DIFFUSION, SITTING DROP PH 7.1, 315 K SODIUM CITRATE, HEPES
Resolution 2.20 Å R-free 0.244
1QAK THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA COLI AMINE OXIDASE : X-RAY CRYSTALLOGRAPHIC STUDIES WITH MUTATIONAL VARIANTS Deposited 1999-03-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–757（722 aa）
Chain B 36–757（722 aa）
Mutation：D383A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D383A Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；pH 7.1
Resolution 2.00 Å R-free 0.244
1QAL THE ACTIVE SITE BASE CONTROLS COFACTOR REACTIVITY IN ESCHERICHIA COLI AMINE OXIDASE : X-RAY CRYSTALLOGRAPHIC STUDIES WITH MUTATIONAL VARIANTS Deposited 1999-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–756（721 aa）
Chain B 36–756（721 aa）
Mutation：D383N Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D383N Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；315 K；VAPOR DIFFUSION, SITTING DROP, PH 7.1, 315K, 1.2 M SODIUM CITRATE, 0.1 M HEPES CRYOPROTECTANT 1.4 M SODIUM CITRATE 0.1M HEPES 20% GLYCEROL
Resolution 2.20 Å R-free 0.241
1SPU STRUCTURE OF OXIDOREDUCTASE Deposited 1996-11-13 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2 PROTEIN SOLUTION CONCENTRATION 6.5 MG/ML INHIBITOR SOAKING SOLUTION 0.375MM 2-HYDRAZINOPYRIDINE MADE UP IN 1.4M SODIUM CITRATE, 0.1M HEPES BUFFER, PH 7.2. CRYSTAL SOAKED FOR 30 DAYS. CRYOPROTECTANT 20% GLYCEROL, 1.44M SODIUM CITRATE BUFFER, PH 6.4
Resolution 2.00 Å
2W0Q E. coli copper amine oxidase in complex with Xenon Deposited 2008-08-20 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 4 XE XENON × 11 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.1；100MM HEPES, PH 7.1, 1.2 M SODIUM CITRATE
Resolution 2.48 Å R-free 0.219
2WGQ Zinc substituted E Coli Copper Amine Oxidase, a model for the precursor for 2,4,5-trihydroxyphenylalaninequinone formation Deposited 2009-04-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Not recorded ZN ZINC ION × 2 CA CALCIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å R-free 0.264
2WO0 EDTA treated E. coli copper amine oxidase Deposited 2009-07-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa） Fragment：RESIDUES 31-757
Chain B 31–757（727 aa） Fragment：RESIDUES 31-757
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 conditions Resolution 2.60 Å R-free 0.248
2WOF EDTA treated E. coli copper amine oxidase Deposited 2009-07-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 conditions Resolution 2.25 Å R-free 0.220
2WOH Strontium soaked E. coli copper amine oxidase Deposited 2009-07-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–757（727 aa）
Chain B 31–757（727 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 CA CALCIUM ION × 2 SR STRONTIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.243

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 6ezz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ezz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ezz
Deposition date deposition_date2017-11-16
Structure title titleCrystal structure of Escherichia coli amine oxidase mutant E573Q
Keywords keywordsOXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.92 Å
Radius of gyration Rg (electron density) rg_electron33.22 Å
Forward intensity I(0) i0397184000.00
Molecular weight molecular_weight161790.0 kDa
Excluded volume excluded_volume202540 ų
Envelope volume envelope_volume246000 ų
Hydration-shell volume shell_volume58467 ų
Envelope diameter envelope_diameter115.2 Å
Shell Rg shell_rg42.27 Å
Envelope Rg envelope_rg33.51 Å
Shape Rg shape_rg33.19 Å
Total Rg total_rg33.92 Å
Total atoms total_atoms11401
Residues n_residues1438
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.2 Å
Rg (real space) rg_real33.76 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real3.9720e+08
I(0) uncertainty (real space) i0_real_error6.2700e+06
Rg (reciprocal space) rg_reciprocal33.86 Å
I(0) (reciprocal space) i0_reciprocal397200000.0000
Solution quality estimate total_estimate0.8972
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.5 Å
Skewness Skewness skewness0.186
Kurtosis Kurtosis kurtosis-0.427
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115500000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.933
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd6ezza1
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.82.1.0 — automated matches
Domain ID domain_idd6ezza2
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.17.2.0 — automated matches
Domain ID domain_idd6ezza3
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.17.2.0 — automated matches
Domain ID domain_idd6ezza4
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_idd6ezzb1
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.82.1.0 — automated matches
Domain ID domain_idd6ezzb2
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.17.2.0 — automated matches
Domain ID domain_idd6ezzb3
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.17.2.0 — automated matches
Domain ID domain_idd6ezzb4
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_id6ezzA01
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_id6ezzA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40 —
Domain ID domain_id6ezzA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40 —
Domain ID domain_id6ezzA04
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_id6ezzB01
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_id6ezzB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40 —
Domain ID domain_id6ezzB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40 —
Domain ID domain_id6ezzB04
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
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8. Citations (1)

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9. Files and Curves (10)