SAXSdb — 3epn

▼

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

Thiamine biosynthesis protein thiC

Caulobacter crescentus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIC_CAUCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–612； UniProt 1–612 Author chain B； PDBConstruct 1–612； UniProt 1–612

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3epn
Deposition date deposition_date	2008-09-29
Structure title title	Crystal structure of Caulobacter crescentus ThiC complexed with imidazole ribonucleotide
Keywords keywords	Alpha-Beta Barrel, SAM superfamily, Thiamine biosynthesis, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3epn__assembly_1__model_1

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

Download this curve (.dat)

3epn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3epn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.20 Å
Rg (electron density)	30.52 Å
Total Rg	31.15 Å
Atom count	8191
Residues	1042
Excluded volume	144890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3epn__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Thiamine biosynthesis protein thiC
Molecular weight formula_weight	68056.1 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	8715

MNIQSTIKAVAETISTGPIPGSRKVYQAGELFPELRVPFREVAVHPSANEPPVTIYDPSGPYSDPAIQIDIEKGLPRTREALVVARGDVEEVADPRQVKPEDNGFAQGKHLAPEFPDTGRKIYRAKPGKLVTQLEYARAGIITAEMEYVAIRENLRREQDRPCVRDGEDFGASIPDFVTPEFVRQEIARGRAIIPANINHGELEPMAIGRNFLVKINANIGNSAVLSTVADEVDKLVWATRWGADTVMDLSTGRNIHNIRDWIIRNSSVPIGTVPIYQALEKVNGVAEDLNWEVFRDTLIEQCEQGVDYFTIHAGVRLPFIPMTAKRVTGIVSRGGSIMAKWCLAHHKENFLYERFDEICEIMRAYDVSFSLGDGLRPGSTADANDEAQFSELRTLGELTKVAWKHGVQVMIEGPGHVAMHKIKANMDEQLKHCHEAPFYTLGPLTTDIAPGYDHITSAIGAAMIGWFGTAMLCYVTPKEHLGLPDRDDVKTGVITYKLAAHAADLAKGHPGAAMWDDAISRARFEFRWEDQFNLGLDPETARKFHDETLPKEAHKTAHFCSMCGPKFCSMKISQEVRDFAAGKAPNSAELGMAEMSEKFREQGSEIYLKTE

Source Source

Source organism organism	Caulobacter crescentus
NCBI taxonomy ID ncbi_taxonomy_id	155892
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole
Molecular weight formula_weight	280.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	513

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3epnA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	540 — Radical SAM ThiC family, central domain

Domain ID domain_id	3epnA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	620 —

Domain ID domain_id	3epnB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	540 — Radical SAM ThiC family, central domain

Domain ID domain_id	3epnB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	620 —

▶

Unit-cell length a length_a	62.603 Å
Unit-cell length b length_b	102.738 Å
Unit-cell length c length_c	82.635 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.05 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	35.240 Å
R factor r_factor	0.1720
R_work r_work	0.1680
R_free r_free	0.2490

Crystal structure of Caulobacter crescentus ThiC complexed with imidazole ribonucleotide

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

Thiamine biosynthesis protein thiC

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

3epn__assembly_1__model_1

3epn__assembly_1__model_1 | I(q)

3epn__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Caulobacter crescentus ThiC complexed with imidazole ribonucleotide

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

Thiamine biosynthesis protein thiC

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

3epn__assembly_1__model_1

3epn__assembly_1__model_1 | I(q)

3epn__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)