SAXSdb — 3fmi

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

Dethiobiotin synthetase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 7-KETO-8-AMINOPELARGONIC ACID × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 7-KETO-8-AMINOPELARGONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIOD_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–251； UniProt 1–226 Author chain B； PDBConstruct 26–251； UniProt 1–226 Author chain C； PDBConstruct 26–251； UniProt 1–226 Author chain D； PDBConstruct 26–251； UniProt 1–226

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	3fmi
Deposition date deposition_date	2008-12-22
Structure title title	Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-Keto 8-aminopelargonic acid
Keywords keywords	Rv1570, bioD, Ligase, ATP-binding, Biotin biosynthesis, Magnesium, Nucleotide-binding; LIGASE
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.

3fmi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3fmi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fmi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.05 Å
Rg (electron density)	22.88 Å
Total Rg	23.63 Å
Atom count	3169
Residues	449
Excluded volume	56652 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fmi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fmi__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Dethiobiotin synthetase
Molecular weight formula_weight	25331.9 kDa
EC 编号 ec_number	6.3.3.3
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	6599

MGSSHHHHHHSSGLQGTENLYFQSHMTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDDLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLDRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHTKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAGAASLDAGDFAAMSAAAFDRNWVAGLVG

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	7-KETO-8-AMINOPELARGONIC ACID
Molecular weight formula_weight	187.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3fmiA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3fmiB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3fmiC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3fmiD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	55.372 Å
Unit-cell length b length_b	105.137 Å
Unit-cell length c length_c	151.569 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	2.180 Å
Low-resolution limit resolution_low	32.000 Å
R factor r_factor	0.2164
R_work r_work	0.2138
R_free r_free	0.2643

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-Keto 8-aminopelargonic acid

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

Dethiobiotin synthetase

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

3fmi__assembly_2__model_1

3fmi__assembly_2__model_1 | I(q)

3fmi__assembly_2__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 non-polymer

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)

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with 7-Keto 8-aminopelargonic acid

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

Dethiobiotin synthetase

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

3fmi__assembly_2__model_1

3fmi__assembly_2__model_1 | I(q)

3fmi__assembly_2__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 non-polymer

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)