SAXSdb — 2y3s

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

TAML

STREPTOMYCES SP. 307-9

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 TIRANDAMYCIN E × 2 MAGNESIUM ION × 2 GLYCEROL × 5 CHLORIDE ION × 5 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3Y1I2_9ACTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 31–530； UniProt 1–500 Author chain B； PDBConstruct 31–530； UniProt 1–500

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	2y3s
Deposition date deposition_date	2010-12-23
Structure title title	Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase TamL in C2 space group
Keywords keywords	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.

2y3s__assembly_1__model_1

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

Download this curve (.dat)

2y3s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y3s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.56 Å
Rg (electron density)	28.34 Å
Total Rg	29.11 Å
Atom count	7800
Residues	990
Excluded volume	136760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y3s__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 (7)

Entity 1 Entity 1 polymer

Description description	TAML
Molecular weight formula_weight	58189.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8851

MGSHHHHHHHHGSDYDIPTTENLYFQGSEFMKHIDSVAPGDIRYEDLRRGENLRFVGDPEEIHLVGSAAEIEQVLSRAVRSGKRVAVRSGGHCYEDFVANSDVRVVMDMSRLSAVGFDEERGAFAVEAGATLGAVYKTLFRVWGVTLPGGACPDVGAGGHILGGGYGPLSRMHGSIVDYLHAVEVVVVDASGDARTVIATREPSDPNHDLWWAHTGGGGGNFGVVVRYWLRTAEADVPPEPGRLLPRPPAEVLLNTTVWPWEGLDEAAFARLVRNHGRWFEQNSGPDSPWCDLYSVLALTRSQSGALAMTTQLDATGPDAEKRLETYLAAVSEGVGVQPHSDTRRLPWLHSTRWPGIAGDGDMTGRAKIKAAYARRSFDDRQIGTLYTRLTSTDYDNPAGVVALIAYGGKVNAVPADRTAVAQRDSILKIVYVTTWEDPAQDPVHVRWIRELYRDVYADTGGVPVPGGAADGAYVNYPDVDLADEEWNTSGVPWSELYYKDAYPRLQAVKARWDPRNVFRHALSVRVPPA

Source Source

Source organism organism	STREPTOMYCES SP. 307-9
NCBI taxonomy ID ncbi_taxonomy_id	529089
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	2

Entity 3 Entity 3 non-polymer

Description description	TIRANDAMYCIN E
Molecular weight formula_weight	403.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	888

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2y3sA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2y3sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2y3sB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2y3sB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	162.046 Å
Unit-cell length b length_b	105.786 Å
Unit-cell length c length_c	70.971 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	86.760 Å
R factor r_factor	0.1636
R_work r_work	0.1606
R_free r_free	0.2204

Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase TamL in C2 space group

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

TAML

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

2y3s__assembly_1__model_1

2y3s__assembly_1__model_1 | I(q)

2y3s__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the tirandamycine-bound FAD-dependent tirandamycin oxidase TamL in C2 space group

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

TAML

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

2y3s__assembly_1__model_1

2y3s__assembly_1__model_1 | I(q)

2y3s__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)