SAXSdb — 4yvz

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

DNA integrity scanning protein DisA

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	MANGANESE (II) ION × 16 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DISA_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–377； UniProt 1–357 Author chain B； PDBConstruct 21–377； UniProt 1–357

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	4yvz
Deposition date deposition_date	2015-03-20
Structure title title	Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+
Keywords keywords	c-di-AMP synthesis, DAC domain, Inhibitor, pre-reaction state, DNA binding protein, TRANSFERASE; DNA 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.

4yvz__assembly_1__model_1

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

Download this curve (.dat)

4yvz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yvz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	53.34 Å
Rg (electron density)	53.90 Å
Total Rg	53.87 Å
Atom count	22632
Residues	2792
Excluded volume	406690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yvz__assembly_1__model_1`	Octameric （8）	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	DNA integrity scanning protein DisA
Molecular weight formula_weight	42764.0 kDa
EC 编号 ec_number	2.7.7.85
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5775

MGSSHHHHHHSSGLVPRGSHMGVKSLVPQELIEKIKLISPGTELRKALDDIINANFGALIFLVDDPKKYEDVIQGGFWLDTDFSAEKLYELSKMDGAIVLSEDITKIYYANVHLVPDPTIPTGETGTRHRTAERLAKQTGKVVIAVSRRRNIISLYYKNYKYVVNQVDFLISKVTQAISTLEKYKDNFNKLLSELEVLELENRVTLADVVRTLAKGFELLRIVEEIRPYIVELGEEGRLARMQLRELTEDVDDLLVLLIMDYSSEEVEEETAQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISSLKHRKTSE

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4yvzA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1700 — YojJ-like (1
Homologous superfamily homologous superfamily	10 — DNA integrity scanning protein, DisA, N-terminal domain

Domain ID domain_id	4yvzA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	110 — DNA integrity scanning linker region

Domain ID domain_id	4yvzA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	4yvzB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1700 — YojJ-like (1
Homologous superfamily homologous superfamily	10 — DNA integrity scanning protein, DisA, N-terminal domain

Domain ID domain_id	4yvzB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	110 — DNA integrity scanning linker region

Domain ID domain_id	4yvzB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

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Unit-cell length a length_a	107.490 Å
Unit-cell length b length_b	107.490 Å
Unit-cell length c length_c	168.790 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 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.495 Å
Low-resolution limit resolution_low	168.790 Å
R factor r_factor	0.1670
R_work r_work	0.1642
R_free r_free	0.2189

Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+

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

DNA integrity scanning protein DisA

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

4yvz__assembly_1__model_1

4yvz__assembly_1__model_1 | I(q)

4yvz__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+

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

DNA integrity scanning protein DisA

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

4yvz__assembly_1__model_1

4yvz__assembly_1__model_1 | I(q)

4yvz__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 (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) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)