SAXSdb — 2yg5

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

PUTRESCINE OXIDASE

RHODOCOCCUS ERYTHROPOLIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 SULFATE ION × 6 GLYCEROL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B0F9F6_RHOER
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–453； UniProt 1–453

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	2yg5
Deposition date deposition_date	2011-04-11
Structure title title	Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C mutant
Keywords keywords	OXIDOREDUCTASE, FLAVIN; 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.

2yg5__assembly_1__model_1

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

Download this curve (.dat)

2yg5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yg5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.66 Å
Rg (electron density)	35.79 Å
Total Rg	36.10 Å
Atom count	7086
Residues	900
Excluded volume	124060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yg5__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	PUTRESCINE OXIDASE
Molecular weight formula_weight	49429.0 kDa
EC 编号 ec_number	1.4.3.10
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3897

VPTLQRDVAIVGAGPSGLAAATALRKAGLSVAVIEARDRVGGRTWTDTIDGAVLEIGGQWVSPDQTALISLLDELGLKTFERYREGESVYISSAGERTRYTGDSFPTNETTKKEMDRLIDEMDDLAAQIGAEEPWAHPLARDLDTVSFKQWLINQSDDAEARDNIGLFIAGGMLTKPAHSFSALQAVLMAASAGSFSHLVDEDFILDKRVIGGMQQVSIRMAEALGDDVFLNAPVRTVKWNESGATVLADGDIRVEASRVILAVPPNLYSRISYDPPLPRRQHQMHQHQSLGLVIKVHAVYETPFWREDGLSGTGFGASEVVQEVYDNTNHEDDRGTLVAFVSDEKADAMFELSAEERKATILASLARYLGPKAEEPVVYYESDWGSEEWTRGCYAASFDLGGLHRYGADSRTPVGPIHFSCSDIAAEGYQHVDGAVRMGQRTAADIIARSKA

Source Source

Source organism organism	RHODOCOCCUS ERYTHROPOLIS
NCBI taxonomy ID ncbi_taxonomy_id	1833
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	2yg5A01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	2yg5A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	660 — Polyamine Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2yg5A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	405 — Guanine Nucleotide Dissociation Inhibitor; domain 1
Homologous superfamily homologous superfamily	10 — Guanine Nucleotide Dissociation Inhibitor, domain 1

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Unit-cell length a length_a	102.003 Å
Unit-cell length b length_b	102.003 Å
Unit-cell length c length_c	130.361 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	102.060 Å
R factor r_factor	0.1999
R_work r_work	0.1978
R_free r_free	0.2425

Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C mutant

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

PUTRESCINE 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

2yg5__assembly_1__model_1

2yg5__assembly_1__model_1 | I(q)

2yg5__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Structure-based redesign of cofactor binding in Putrescine Oxidase: A394C mutant

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

PUTRESCINE 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

2yg5__assembly_1__model_1

2yg5__assembly_1__model_1 | I(q)

2yg5__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)