SAXSdb — 2xm3

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

TRANSPOSASE

DEINOCOCCUS RADIODURANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 4	DRA2 TRANSPOSASE BINDING ELEMENT × 2 5'-D(TPTPAPGP*T)-3' × 2 MAGNESIUM ION × 4 GLYCEROL × 1 water × 6	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 4	DRA2 TRANSPOSASE BINDING ELEMENT × 2 5'-D(TPTPAPGP*T)-3' × 2 ACETATE ION × 1 MAGNESIUM ION × 4 GLYCEROL × 2 water × 6	Consistent with all polymers
3	Protein–DNA	Homooligomer	Protein 2 DNA 4	DRA2 TRANSPOSASE BINDING ELEMENT × 2 5'-D(TPTPAPGP*T)-3' × 2 MAGNESIUM ION × 4 GLYCEROL × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O83028_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–140； UniProt 1–140 Author chain B； PDBConstruct 1–140； UniProt 1–140 Author chain C； PDBConstruct 1–140； UniProt 1–140 Author chain D； PDBConstruct 1–140； UniProt 1–140 Author chain E； PDBConstruct 1–140； UniProt 1–140 Author chain F； PDBConstruct 1–140； UniProt 1–140

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	2xm3
Deposition date deposition_date	2010-07-22
Structure title title	Deinococcus radiodurans ISDra2 Transposase Left end DNA complex
Keywords keywords	DNA BINDING PROTEIN-DNA COMPLEX, TRANSPOSITION, MOBILE ELEMENT; DNA BINDING PROTEIN/DNA
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.

2xm3__assembly_2__model_1

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

Download this curve (.dat)

2xm3__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xm3__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.80 Å
Rg (electron density)	23.63 Å
Total Rg	24.37 Å
Atom count	3371
Residues	319
Excluded volume	56534 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xm3__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xm3__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xm3__assembly_3__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 (7)

Entity 1 Entity 1 polymer

Description description	TRANSPOSASE
Molecular weight formula_weight	16135.8 kDa
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	10596

MTYVILPLEMKKGRGYVYQLEYHLIWCVKYRHQVLVGEVADGLKDILRDIAAQNGLEVITMEVMPDHVHLLLSATPQQAIPDFVKALKGASARRMFVAYPQLKEKLWGGNLWNPSYCILTVSENTRAQIQKYIESQHDKE

Source Source

Source organism organism	DEINOCOCCUS RADIODURANS
NCBI taxonomy ID ncbi_taxonomy_id	1299
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	DRA2 TRANSPOSASE BINDING ELEMENT
Molecular weight formula_weight	8252.3 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,I,K,M,O,Q

CGCACACTCGTGACTTCAGTCATGAGT

Entity 3 Entity 3 polymer

Description description	5'-D(TPTPAPGP*T)-3'
Molecular weight formula_weight	1510.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	H,J,L,N,P,R

TTGAT

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	509

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2xm3A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2xm3B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2xm3C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2xm3D00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2xm3E00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2xm3F00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

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Unit-cell length a length_a	104.583 Å
Unit-cell length b length_b	128.384 Å
Unit-cell length c length_c	140.222 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	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2179
R_work r_work	0.2179
R_free r_free	0.2489

Deinococcus radiodurans ISDra2 Transposase Left end DNA complex

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

TRANSPOSASE

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

2xm3__assembly_2__model_1

2xm3__assembly_2__model_1 | I(q)

2xm3__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Deinococcus radiodurans ISDra2 Transposase Left end DNA complex

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

TRANSPOSASE

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

2xm3__assembly_2__model_1

2xm3__assembly_2__model_1 | I(q)

2xm3__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)