SAXSdb — 2tdx

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

DIPHTHERIA TOX REPRESSOR

Corynebacterium diphtheriae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DTXR_CORDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–226； UniProt 1–226

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	2tdx
Deposition date deposition_date	1998-06-22
Structure title title	DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL
Keywords keywords	;DNA-BINDING REGULATORY PROTEIN, DIPHTHERIA TOX REPRESSOR, TRANSCRIPTION REGULATION, DNA-BINDING PROTEIN, IRON-REGULATED REPRESSOR, DNA BINDING PROTEIN ;; 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.

2tdx__assembly_1__model_1

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

Download this curve (.dat)

2tdx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2tdx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.11 Å
Rg (electron density)	20.22 Å
Total Rg	20.93 Å
Atom count	2206
Residues	278
Excluded volume	39226 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2tdx__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	DIPHTHERIA TOX REPRESSOR
Molecular weight formula_weight	25361.7 kDa
Mutation mutation	C102D
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	1129

MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL

Source Source

Source organism organism	Corynebacterium diphtheriae
NCBI taxonomy ID ncbi_taxonomy_id	1717
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2tdxa1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.24 — Iron-dependent repressor protein

Domain ID domain_id	d2tdxa2
Class class	a — All alpha proteins
Fold Fold fold	a.76 — Iron-dependent repressor protein, dimerization domain
Superfamily Superfamily superfamily	a.76.1 — Iron-dependent repressor protein, dimerization domain
Family Family family	a.76.1.1 — Iron-dependent repressor protein, dimerization domain

CATH v4.4 (2 domains)

Domain ID domain_id	2tdxA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2tdxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	60 — Diphtheria Toxin Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Iron dependent repressor, metal binding and dimerisation domain

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Unit-cell length a length_a	64.500 Å
Unit-cell length b length_b	64.500 Å
Unit-cell length c length_c	105.700 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2460
R_work r_work	0.2460
R_free r_free	0.3210

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

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

DIPHTHERIA TOX REPRESSOR

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

2tdx__assembly_1__model_1

2tdx__assembly_1__model_1 | I(q)

2tdx__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL

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

DIPHTHERIA TOX REPRESSOR

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

2tdx__assembly_1__model_1

2tdx__assembly_1__model_1 | I(q)

2tdx__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)