3mle

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Method: X-RAY DIFFRACTION

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

Dethiobiotin synthetase

Helicobacter pylori

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 MAGNESIUM ION × 2 NITRATE ION × 1 CHLORIDE ION × 2 8-aminooctanoic acid × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 MAGNESIUM ION × 2 NITRATE ION × 1 8-aminooctanoic acid × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 2 MAGNESIUM ION × 2 NITRATE ION × 1 CHLORIDE ION × 1 8-aminooctanoic acid × 2 ADENOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIOD_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–240； UniProt 1–218 Author chain B； PDBConstruct 23–240； UniProt 1–218 Author chain C； PDBConstruct 23–240； UniProt 1–218 Author chain D； PDBConstruct 23–240； UniProt 1–218 Author chain E； PDBConstruct 23–240； UniProt 1–218 Author chain F； PDBConstruct 23–240； UniProt 1–218

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	3mle
Deposition date deposition_date	2010-04-16
Structure title title	Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP
Keywords keywords	;DTBS, dethiobiotin synthetase, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, LIGASE ;; 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.

3mle__assembly_1__model_1

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

Download this curve (.dat)

3mle__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3mle__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.35 Å
Rg (electron density)	23.38 Å
Total Rg	24.11 Å
Atom count	3525
Residues	444
Excluded volume	62840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3mle__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3mle__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3mle__assembly_3__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 (8)

Entity 1 Entity 1 polymer

Description description	Dethiobiotin synthetase
Molecular weight formula_weight	27148.1 kDa
EC 编号 ec_number	6.3.3.3
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10803

MGSSHHHHHHSSGRENLYFQGHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALKGS

Source Source

Source organism organism	Helicobacter pylori
Common name common_name	Campylobacter pylori
NCBI taxonomy ID ncbi_taxonomy_id	85962
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	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	8-aminooctanoic acid
Molecular weight formula_weight	159.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3mleA00
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	3mleB00
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	3mleC00
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	3mleD00
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	3mleE00
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	3mleF00
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	79.773 Å
Unit-cell length b length_b	131.905 Å
Unit-cell length c length_c	133.099 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2460

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

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

3mle__assembly_1__model_1

3mle__assembly_1__model_1 | I(q)

3mle__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

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

3mle__assembly_1__model_1

3mle__assembly_1__model_1 | I(q)

3mle__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)