SAXSdb — 3fnn

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

Thymidylate synthase thyX

Corynebacterium glutamicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_CORGL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–256； UniProt 1–250

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	3fnn
Deposition date deposition_date	2008-12-26
Structure title title	Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis
Keywords keywords	ThyX, thymidylate synthase, FAD, Flavoprotein, Methyltransferase, Nucleotide biosynthesis, Transferase; TRANSFERASE
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.

3fnn__assembly_1__model_1

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

Download this curve (.dat)

3fnn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fnn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.36 Å
Rg (electron density)	28.66 Å
Total Rg	29.39 Å
Atom count	7372
Residues	908
Excluded volume	129160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fnn__assembly_1__model_1`	tetrameric （4）	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	Thymidylate synthase thyX
Molecular weight formula_weight	28928.6 kDa
EC 编号 ec_number	2.1.1.148
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	1921

HHHHHHMAEQVKLSVELIACSSFTPPADVEWSTDVEGAEALVEFAGRACYETFDKPNPRTASNAAYLRHIMEVGHTALLEHANATMYIRGISRSATHELVRHRHFSFSQLSQRFVHSGESEVVVPTLIDEDPQLRELFMHAMDESRFAFNELLNALEEKLGDEPNALLRKKQARQAARAVLPNATESRIVVSGNFRTWRHFIGMRASEHADVEIREVAVECLRKLQVAAPTVFGDFEIETLADGSQMATSPYVMDF

Source Source

Source organism organism	Corynebacterium glutamicum
Common name common_name	Brevibacterium flavum
NCBI taxonomy ID ncbi_taxonomy_id	1718
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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3fnnA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3180 —

Domain ID domain_id	3fnnA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3fnnA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

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Unit-cell length a length_a	95.806 Å
Unit-cell length b length_b	95.806 Å
Unit-cell length c length_c	64.637 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 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	27.430 Å
R factor r_factor	0.2245
R_work r_work	0.2227
R_free r_free	0.2595

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

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

Thymidylate synthase thyX

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

3fnn__assembly_1__model_1

3fnn__assembly_1__model_1 | I(q)

3fnn__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 (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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Biochemical and structural analysis of an atypical ThyX: Corynebacterium glutamicum NCHU 87078 depends on ThyA for thymidine biosynthesis

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

Thymidylate synthase thyX

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

3fnn__assembly_1__model_1

3fnn__assembly_1__model_1 | I(q)

3fnn__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 (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) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)