SAXSdb — 4qz8

▼

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

DNA nucleotidylexotransferase

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 3	5'-D(APAPAPAPAPC)-3' × 2 5'-D(TPTPTPTPTPGP*G)-3' × 1 MAGNESIUM ION × 1 SODIUM ION × 1 ;2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE ; × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDT_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–372； UniProt 132–482 Author chain A； PDBConstruct 373–400； UniProt 503–530

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4qz8
Deposition date deposition_date	2014-07-27
Structure title title	Mouse Tdt in complex with a DSB substrate, C-G base pair
Keywords keywords	Terminal deoxynucleotidyltransferase, nucleus, TRANSFERASE-DNA complex; TRANSFERASE/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4qz8__assembly_1__model_1

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

Download this curve (.dat)

4qz8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qz8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.56 Å
Rg (electron density)	21.85 Å
Total Rg	22.59 Å
Atom count	3038
Residues	365
Excluded volume	52477 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qz8__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	DNA nucleotidylexotransferase
Molecular weight formula_weight	45704.0 kDa
EC 编号 ec_number	2.7.7.31
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3149

MGSSHHHHHHSSGLVPRGSHMSPSPVPGSQNVPAPAVKKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITSPEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDHFQKCFLILKLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHALYDRTKRVFLEAESEEEIFAHLGLDYIEPWERNA

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(APAPAPAPAPC)-3'
Molecular weight formula_weight	1810.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,U

AAAAAC

Entity 3 Entity 3 polymer

Description description	5'-D(TPTPTPTPTPGP*G)-3'
Molecular weight formula_weight	2134.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TTTTTGG

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	;2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	451.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

▼

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4qz8a1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.6 — DNA polymerase beta, N-terminal domain-like
Family Family family	a.60.6.0 — automated matches

Domain ID domain_id	d4qz8a2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.12 — PsbU/PolX domain-like
Family Family family	a.60.12.0 — automated matches

Domain ID domain_id	d4qz8a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.218 — Nucleotidyltransferase
Superfamily Superfamily superfamily	d.218.1 — Nucleotidyltransferase
Family Family family	d.218.1.2 — DNA polymerase beta-like

CATH v4.4 (4 domains)

Domain ID domain_id	4qz8A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	4qz8A02
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	4qz8A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	4qz8A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

▶

Unit-cell length a length_a	59.329 Å
Unit-cell length b length_b	74.259 Å
Unit-cell length c length_c	118.969 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	31.410 Å
R factor r_factor	0.2054
R_work r_work	0.2037
R_free r_free	0.2369

Mouse Tdt in complex with a DSB substrate, C-G base pair

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

DNA nucleotidylexotransferase

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

4qz8__assembly_1__model_1

4qz8__assembly_1__model_1 | I(q)

4qz8__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 (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) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Mouse Tdt in complex with a DSB substrate, C-G base pair

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

DNA nucleotidylexotransferase

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

4qz8__assembly_1__model_1

4qz8__assembly_1__model_1 | I(q)

4qz8__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 (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) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)