SAXSdb — 5jfe

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

Thymidylate synthase ThyX

Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

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 ;2'-deoxy-5'-uridylic acid ; × 4 1,2-ETHANEDIOL × 20 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–232； UniProt 1–220

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	5jfe
Deposition date deposition_date	2016-04-19
Structure title title	Flavin-dependent thymidylate synthase with H2-dUMP
Keywords keywords	thymidylate synthase, complex, H2-dUMP ligand, 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.

5jfe__assembly_1__model_1

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

Download this curve (.dat)

5jfe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jfe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.67 Å
Rg (electron density)	28.29 Å
Total Rg	29.07 Å
Atom count	7456
Residues	852
Excluded volume	133120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jfe__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 (5)

Entity 1 Entity 1 polymer

Description description	Thymidylate synthase ThyX
Molecular weight formula_weight	27503.7 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	2103

MGSDKIHHHHHHMKIDILDKGFVELVDVMGNDLSAVRAARVSFDMGLKDEERDRHLIEYLMKHGHETPFEHIVFTFHVKAPIFVARQWFRHRIASYNELSGRYSKLSYEFYIPSPERLEGYKTTIPPERVTEKISEIVDKAYRTYLELIESGVPREVARIVLPLNLYTRFFWTVNARSLMNFLNLRADSHAQWEIQQYALAIARIFKEKCPWTFEAFLKYAYKGDILKEVQV

Source Source

Source organism organism	Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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	;2'-deoxy-5'-uridylic acid ;
Molecular weight formula_weight	310.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5jfea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.207 — Thymidylate synthase-complementing protein Thy1
Superfamily Superfamily superfamily	d.207.1 — Thymidylate synthase-complementing protein Thy1
Family Family family	d.207.1.1 — Thymidylate synthase-complementing protein Thy1

Domain ID domain_id	d5jfea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	5jfeA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	110.322 Å
Unit-cell length b length_b	110.322 Å
Unit-cell length c length_c	120.765 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	47.750 Å
R factor r_factor	0.1710
R_work r_work	0.1700
R_free r_free	0.1900

Flavin-dependent thymidylate synthase with H2-dUMP

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

5jfe__assembly_1__model_1

5jfe__assembly_1__model_1 | I(q)

5jfe__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

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Flavin-dependent thymidylate synthase with H2-dUMP

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

5jfe__assembly_1__model_1

5jfe__assembly_1__model_1 | I(q)

5jfe__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

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)