SAXSdb — 3ere

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

Arginine repressor

Mycobacterium tuberculosis

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	5'-D(DTPDTPDGPDCPDAPDTPDAPDAPDCPDGPDAPDTPDGPDCPDAPDA)-3' × 2 5'-D(DTPDTPDGPDCPDAPDTPDCPDGPDTPDTPDAPDTPDGPDCPDAPDA)-3' × 2 SULFATE ION × 6 water × 6	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DTPDTPDGPDCPDAPDTPDAPDAPDCPDGPDAPDTPDGPDCPDAPDA)-3' × 1 5'-D(DTPDTPDGPDCPDAPDTPDCPDGPDTPDTPDAPDTPDGPDCPDAPDA)-3' × 1 SULFATE ION × 3 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARGR_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain D； PDBConstruct 1–170； UniProt 1–170

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	3ere
Deposition date deposition_date	2008-10-01
Structure title title	Crystal structure of the arginine repressor protein from Mycobacterium tuberculosis in complex with the DNA operator
Keywords keywords	;Mycobacterium tuberculosis, arginine repressor protein, DNA binding, ArgR-operator complex, Structural Genomics, TB structural genomics, TB Structural Genomics Consortium, TBSGC, Amino-acid biosynthesis, Arginine biosynthesis, DNA-binding, Transcription, Transcription regulation, DNA BINDING PROTEIN-DNA COMPLEX ;; 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.

3ere__assembly_2__model_1

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

Download this curve (.dat)

3ere__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ere__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.82 Å
Rg (electron density)	20.97 Å
Total Rg	21.69 Å
Atom count	1787
Residues	188
Excluded volume	29543 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ere__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ere__assembly_2__model_1`	trimeric （3）	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 (5)

Entity 1 Entity 1 polymer

Description description	Arginine repressor
Molecular weight formula_weight	17366.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	1880

MSRAKAAPVAGPEVAANRAGRQARIVAILSSAQVRSQNELAALLAAEGIEVTQATLSRDLEELGAVKLRGADGGTGIYVVPEDGSPVRGVSGGTDRMARLLGELLVSTDDSGNLAVLRTPPGAAHYLASAIDRAALPQVVGTIAGDDTILVVAREPTTGAQLAGMFENLR

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(DTPDTPDGPDCPDAPDTPDAPDAPDCPDGPDAPDTPDGPDCPDAPDA)-3'
Molecular weight formula_weight	4906.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A

TTGCATAACGATGCAA

Entity 3 Entity 3 polymer

Description description	5'-D(DTPDTPDGPDCPDAPDTPDCPDGPDTPDTPDAPDTPDGPDCPDAPDA)-3'
Molecular weight formula_weight	4888.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

TTGCATCGTTATGCAA

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ereD01
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	3ereD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	94.128 Å
Unit-cell length b length_b	94.128 Å
Unit-cell length c length_c	147.014 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	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2274
R_work r_work	0.2274
R_free r_free	0.2554

Crystal structure of the arginine repressor protein from Mycobacterium tuberculosis in complex with the DNA operator

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

Arginine 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

3ere__assembly_2__model_1

3ere__assembly_2__model_1 | I(q)

3ere__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the arginine repressor protein from Mycobacterium tuberculosis in complex with the DNA operator

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

Arginine 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

3ere__assembly_2__model_1

3ere__assembly_2__model_1 | I(q)

3ere__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)