SAXSdb — 3hzg

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

Thymidylate synthase thyX

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PHOSPHATE ION × 9 FLAVIN-ADENINE DINUCLEOTIDE × 4 GLYCEROL × 3 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 2 GLYCEROL × 3 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 5 FLAVIN-ADENINE DINUCLEOTIDE × 2 GLYCEROL × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 5 FLAVIN-ADENINE DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THYX_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 1–250 Author chain B； PDBConstruct 1–250； UniProt 1–250 Author chain C； PDBConstruct 1–250； UniProt 1–250 Author chain D； PDBConstruct 1–250； 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	3hzg
Deposition date deposition_date	2009-06-23
Structure title title	Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD
Keywords keywords	;ThyX, FAD, thymidylate synthase, Flavoprotein, Methyltransferase, Nucleotide biosynthesis, Transferase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID ;; 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.

3hzg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3hzg__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hzg__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	26.98 Å
Rg (electron density)	26.38 Å
Total Rg	27.08 Å
Atom count	3959
Residues	490
Excluded volume	69480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hzg__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hzg__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3hzg__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3hzg__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3hzg__assembly_5__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	Thymidylate synthase thyX
Molecular weight formula_weight	28699.4 kDa
EC 编号 ec_number	2.1.1.148
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8129

MAETAPLRVQLIAKTDFLAPPDVPWTTDADGGPALVEFAGRACYQSWSKPNPKTATNAGYLRHIIDVGHFSVLEHASVSFYITGISRSCTHELIRHRHFSYSQLSQRYVPEKDSRVVVPPGMEDDADLRHILTEAADAARATYSELLAKLEAKFADQPNAILRRKQARQAARAVLPNATETRIVVTGNYRAWRHFIAMRASEHADVEIRRLAIECLRQLAAVAPAVFADFEVTTLADGTEVATSPLATEALEHHHHHH

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	9

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	4

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	257

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3hzgA01
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	3hzgA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3hzgA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	3hzgB01
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	3hzgB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3hzgB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	3hzgC01
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	3hzgC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3hzgC03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	440 —

Domain ID domain_id	3hzgD01
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	3hzgD02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	3hzgD03
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	78.553 Å
Unit-cell length b length_b	86.594 Å
Unit-cell length c length_c	162.487 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	43.300 Å
R factor r_factor	0.2020
R_work r_work	0.1980
R_free r_free	0.2730

Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD

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

3hzg__assembly_3__model_1

3hzg__assembly_3__model_1 | I(q)

3hzg__assembly_3__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of mycobacterium tuberculosis thymidylate synthase X bound with FAD

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

3hzg__assembly_3__model_1

3hzg__assembly_3__model_1 | I(q)

3hzg__assembly_3__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)