SAXSdb — 2c5s

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

PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII

BACILLUS ANTHRACIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE MONOPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THII_BACAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–413； UniProt 1–403

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	2c5s
Deposition date deposition_date	2005-11-01
Structure title title	Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain
Keywords keywords	;RNA-BINDING PROTEIN, RNA BINDING PROTEIN, TRNA MODIFICATION, 4-THIOURIDINE SYNTHASE, FERREDOXIN-LIKE DOMAIN, THUMP DOMAIN, PP-LOOP PYROPHOSPHATASE DOMAIN, THIAMINE BIOSYNTHESIS ;; RNA BINDING PROTEIN
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.

2c5s__assembly_1__model_1

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

Download this curve (.dat)

2c5s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c5s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.11 Å
Rg (electron density)	31.47 Å
Total Rg	31.93 Å
Atom count	5974
Residues	744
Excluded volume	107320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c5s__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII
Molecular weight formula_weight	46968.2 kDa
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	3037

MGSSHHHHHHMTYEYILVRYGEMTTKGKNRSKFVSTLKDNVKFKLKKFPNIKIDATHDRMYIQLNGEDHEAVSERLKDVFGIHKFNLAMKVPSELEDIKKGALAAFLQVKGDVKTFKITVHRSYKHFPMRTMELLPEIGGHILENTEDITVDVHNPDVNVRVEIRSGYSYIMCDERMGAGGLPVGVGGKVMVLLSGGIDSPVAAYLTMKRGVSVEAVHFHSPPFTSERAKQKVIDLAQELTKYCKRVTLHLVPFTEVQKTINKEIPSSYSMTVMRRMMMRITERIAEERNALAITTGESLGQVASQTLDSMHTINEVTNYPVIRPLITMDKLEIIKIAEEIGTYDISIRPYEDCCTVFTPASPATKPKREKANRFEAKYDFTPLIDEAVANKETMVLQTVEVVAEEEKFEELF

Source Source

Source organism organism	BACILLUS ANTHRACIS
NCBI taxonomy ID ncbi_taxonomy_id	198094
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 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	50

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2c5sa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.6 — ThiI-like

Domain ID domain_id	d2c5sa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.308 — THUMP domain
Superfamily Superfamily superfamily	d.308.1 — THUMP domain-like
Family Family family	d.308.1.1 — THUMP domain

CATH v4.4 (2 domains)

Domain ID domain_id	2c5sA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2130 — VC0802-like
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	2c5sA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

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Unit-cell length a length_a	81.047 Å
Unit-cell length b length_b	81.047 Å
Unit-cell length c length_c	140.893 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	24.910 Å
R factor r_factor	0.2290
R_work r_work	0.2270
R_free r_free	0.2780

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

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

PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII

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

2c5s__assembly_1__model_1

2c5s__assembly_1__model_1 | I(q)

2c5s__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain

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

PROBABLE THIAMINE BIOSYNTHESIS PROTEIN THII

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

2c5s__assembly_1__model_1

2c5s__assembly_1__model_1 | I(q)

2c5s__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)