SAXSdb — 2r5u

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

Replicative DNA helicase

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GLYCEROL × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAB_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–200； UniProt 1–197 Author chain B； PDBConstruct 4–200； UniProt 1–197 Author chain C； PDBConstruct 4–200； UniProt 1–197 Author chain D； PDBConstruct 4–200； UniProt 1–197 Author chain E； PDBConstruct 4–200； UniProt 1–197 Author chain F； PDBConstruct 4–200； UniProt 1–197

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	2r5u
Deposition date deposition_date	2007-09-04
Structure title title	Crystal structure of the N-terminal domain of DnaB helicase from Mycobacterium tuberculosis
Keywords keywords	;DnaB, helicase, primase, replication, ATP-binding, Autocatalytic cleavage, DNA replication, DNA-binding, Endonuclease, Hydrolase, Intron homing, Nuclease, Nucleotide-binding, Primosome ;; HYDROLASE
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.

2r5u__assembly_1__model_1

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

Download this curve (.dat)

2r5u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.25 Å
Rg (electron density)	42.96 Å
Total Rg	43.32 Å
Atom count	6281
Residues	847
Excluded volume	111400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5u__assembly_1__model_1`	hexameric （6）	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	Replicative DNA helicase
Molecular weight formula_weight	21373.8 kDa
EC 编号 ec_number	3.6.1.-
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	6697

GPHMAVVDDLAPGMDSSPPSEDYGRQPPQDLAAEQSVLGGMLLSKDAIADVLERLRPGDFYRPAHQNVYDAILDLYGRGEPADAVTVAAELDRRGLLRRIGGAPYLHTLISTVPTAANAGYYASIVAEKALLRRLVEAGTRVVQYGYAGAEGADVAEVVDRAQAEIYDVADRRLSEDFVALEDLLQPTMDEIDAIASSGG

Source Source

Source organism organism	Mycobacterium tuberculosis
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	416

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2r5uA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	2r5uB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	2r5uC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	2r5uD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	2r5uE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

Domain ID domain_id	2r5uF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	860 — DNAb Helicase; Chain A
Homologous superfamily homologous superfamily	10 — DNAb Helicase; Chain A

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Unit-cell length a length_a	114.927 Å
Unit-cell length b length_b	114.927 Å
Unit-cell length c length_c	72.393 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	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2316
R_work r_work	0.2293
R_free r_free	0.2746

Crystal structure of the N-terminal domain of DnaB helicase from Mycobacterium tuberculosis

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

Replicative DNA helicase

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

2r5u__assembly_1__model_1

2r5u__assembly_1__model_1 | I(q)

2r5u__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the N-terminal domain of DnaB helicase from Mycobacterium tuberculosis

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

Replicative DNA helicase

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

2r5u__assembly_1__model_1

2r5u__assembly_1__model_1 | I(q)

2r5u__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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)