SAXSdb — 2cfa

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

THYMIDYLATE SYNTHASE

PARAMECIUM BURSARIA CHLORELLA VIRUS 1

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_PBCV1
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–216； UniProt 1–216 Author chain B； PDBConstruct 1–216； UniProt 1–216

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	2cfa
Deposition date deposition_date	2006-02-17
Structure title title	Structure of viral flavin-dependant thymidylate synthase ThyX
Keywords keywords	FDTS, TSCP, FLAVIN DEPENDENT THYMIDYLATE SYNTHASE FAD, FLAVOPROTEIN, NUCLEOTIDE BIOSYNTHESIS, METHYLTRANSFERASE, 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.

2cfa__assembly_1__model_1

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

Download this curve (.dat)

2cfa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2cfa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.20 Å
Rg (electron density)	26.59 Å
Total Rg	27.45 Å
Atom count	6040
Residues	714
Excluded volume	107460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2cfa__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 (4)

Entity 1 Entity 1 polymer

Description description	THYMIDYLATE SYNTHASE
Molecular weight formula_weight	25150.6 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	3201

MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYCIRHKHWSIFETAFMTLELKTSRGIAAQVLRHRSFHFQEFSQRYASVMETPPPHQARFQDHKNRQNSLDTVPEDDQTWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDWVH

Source Source

Source organism organism	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
NCBI taxonomy ID ncbi_taxonomy_id	10506
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	THYMIDYLATE SYNTHASE
Molecular weight formula_weight	25150.6 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	B

MSAKLISVTKPVVEGVNTAEELIAYAARVSNPENQINNKTASGLLKYCIRHKHWSIFETAFMTLELKTSRGIAAQVIRHRSFHFQEFSQRYASVMETPPPHQARFQDHKNRQNSLDTVPEDDQTWWATEQEKLYAQSMELYNKALEKGIAKECARFILPLSTPTTIYMSGTIRDWIHYIELRTSNGTQREHIDLANACKEIFIKEFPSIAKALDWVH

Source Source

Source organism organism	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
NCBI taxonomy ID ncbi_taxonomy_id	10506
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2cfaA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2cfaA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

Domain ID domain_id	2cfaB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	2cfaB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3070 —

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Unit-cell length a length_a	69.264 Å
Unit-cell length b length_b	76.991 Å
Unit-cell length c length_c	93.437 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2150
R_work r_work	0.2130
R_free r_free	0.2620

Structure of viral flavin-dependant thymidylate synthase ThyX

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

THYMIDYLATE SYNTHASE

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

2cfa__assembly_1__model_1

2cfa__assembly_1__model_1 | I(q)

2cfa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of viral flavin-dependant thymidylate synthase ThyX

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

THYMIDYLATE SYNTHASE

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

2cfa__assembly_1__model_1

2cfa__assembly_1__model_1 | I(q)

2cfa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)