SAXSdb — 6fix

▼

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

XRE family transcriptional regulator

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 2	DNA (30-MER) × 1 DNA (30-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A179R2V1_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–105； UniProt 2–99 Author chain B； PDBConstruct 8–105； UniProt 2–99 Author chain D； PDBConstruct 8–105； UniProt 2–99 Author chain E； PDBConstruct 8–105； UniProt 2–99

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	6fix
Deposition date deposition_date	2018-01-19
Structure title title	antitoxin GraA in complex with its operator
Keywords keywords	GraA, HigA, antitoxin, operator, DNA, GraT, HigB; ANTITOXIN
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.

6fix__assembly_1__model_1

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

Download this curve (.dat)

6fix__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fix__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.96 Å
Rg (electron density)	28.24 Å
Total Rg	28.84 Å
Atom count	4036
Residues	441
Excluded volume	67186 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fix__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	XRE family transcriptional regulator
Molecular weight formula_weight	11746.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	4036

MHHHHHHLKNGMRPIHPGEILREEFQKEMGFSAAALARALGVATPTVNNILRERGGVSADMALRLSICLDTTPEFWLNLQTAFDLRTAEQQHGDEIIGSVQRLVA

Source Source

Source organism organism	Pseudomonas putida
Common name common_name	Arthrobacter siderocapsulatus
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	9512.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AAATTAACGAATAACGTTAAGCATTCAGCTC

Entity 3 Entity 3 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	9218.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

AGCTGAATGCTTAACGTTATTCGTTAATTT

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6fixA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	6fixB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	6fixD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	6fixE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

▶

Unit-cell length a length_a	105.550 Å
Unit-cell length b length_b	105.550 Å
Unit-cell length c length_c	149.940 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	43.853 Å
R factor r_factor	0.2480
R_work r_work	0.2460
R_free r_free	0.2857

antitoxin GraA in complex with its operator

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

XRE family transcriptional regulator

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

6fix__assembly_1__model_1

6fix__assembly_1__model_1 | I(q)

6fix__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

antitoxin GraA in complex with its operator

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

XRE family transcriptional regulator

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

6fix__assembly_1__model_1

6fix__assembly_1__model_1 | I(q)

6fix__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)