3nbb

Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha

Method: X-RAY DIFFRACTION

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

Peroxisomal primary amine oxidase

Pichia angusta

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	COPPER (II) ION × 2 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	COPPER (II) ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMO_PICAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–692； UniProt 1–692 Author chain B； PDBConstruct 1–692； UniProt 1–692 Author chain C； PDBConstruct 1–692； UniProt 1–692 Author chain D； PDBConstruct 1–692； UniProt 1–692 Author chain E； PDBConstruct 1–692； UniProt 1–692 Author chain F； PDBConstruct 1–692； UniProt 1–692

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3nbb
Deposition date deposition_date	2010-06-03
Structure title title	Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha
Keywords keywords	amine oxidase, quinoprotein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3nbb__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3nbb__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nbb__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.02 Å
Rg (electron density)	32.29 Å
Total Rg	32.95 Å
Atom count	10480
Residues	1318
Excluded volume	185400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nbb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3nbb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3nbb__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3nbb__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Peroxisomal primary amine oxidase
Molecular weight formula_weight	77696.6 kDa
EC 编号 ec_number	1.4.3.21
Mutation mutation	Y305F
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	34758

MERLRQIASQATAASAAPARPAHPLDPLSTAEIKAATNTVKSYFAGKKISFNTVTLREPARKAYIQWKEQGGPLPPRLAYYVILEAGKPGVKEGLVDLASLSVIETRALETVQPILTVEDLCSTEEVIRNDPAVIEQCVLSGIPANEMHKVYCDPWTIGYDERWGTGKRLQQALVYYRSDEDDSQYSHPLDFCPIVDTEEKKVIFIDIPNRRRKVSKHKHANFYPKHMIEKVGAMRPEAPPINVTQPEGVSFKMTGNVMEWSNFKFHIGFNYREGIVLSDVSYNDHGNVRPIFHRISLSEMIVPFGSPEFPHQRKHALDIGEYGAGYMTNPLSLGCDCKGVIHYLDAHFSDRAGDPITVKNAVCIHEEDDGLLFKHSDFRDNFATSLVTRATKLVVSQIFTAANXEYCLYWVFMQDGAIRLDIRLTGILNTYILGDDEEAGPWGTRVYPNVNAHNHQHLFSLRIDPRIDGDGNSAAACDAKSSPYPLGSPENMYGNAFYSEKTTFKTVKDSLTNYESATGRSWDIFNPNKVNPYSGKPPSYKLVSTQCPPLLAKEGSLVAKRAPWASHSVNVVPYKDNRLYPSGDHVPQWSGDGVRGMREWIGDGSENIDNTDILFFHTFGITHFPAPEDFPLXPAEPITLMLRPRHFFTENPGLDIQPSYAMTTSEAKRAVHKETKDKTSRLAFEGSCCGK

Source Source

Source organism organism	Pichia angusta
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4905
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3174

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	3nbbA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbA03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	3nbbB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbB03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	3nbbC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbC03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	3nbbD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbD02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbD03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	3nbbE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbE02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbE03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	3nbbF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbF02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3nbbF03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

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Unit-cell length a length_a	94.523 Å
Unit-cell length b length_b	232.618 Å
Unit-cell length c length_c	104.146 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	36.130 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2000

Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha

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

Peroxisomal primary amine oxidase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3nbb__assembly_3__model_1

3nbb__assembly_3__model_1 | I(q)

3nbb__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (2)

Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha

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

Peroxisomal primary amine oxidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3nbb__assembly_3__model_1

3nbb__assembly_3__model_1 | I(q)

3nbb__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (2)