2np5

Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.

Method: X-RAY DIFFRACTION

▼

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

Transcriptional regulator

Rhodococcus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	DODECYL-BETA-D-MALTOSIDE × 1 ETHYL DIMETHYL AMMONIO PROPANE SULFONATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	DODECYL-BETA-D-MALTOSIDE × 1 ETHYL DIMETHYL AMMONIO PROPANE SULFONATE × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	DODECYL-BETA-D-MALTOSIDE × 2 ETHYL DIMETHYL AMMONIO PROPANE SULFONATE × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q0S914_RHOSR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 1–203 Author chain B； PDBConstruct 1–203； UniProt 1–203 Author chain C； PDBConstruct 1–203； UniProt 1–203 Author chain D； PDBConstruct 1–203； UniProt 1–203

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	2np5
Deposition date deposition_date	2006-10-26
Structure title title	Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.
Keywords keywords	;tetR family, transcriptional regulator, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, TRANSCRIPTION ;; TRANSCRIPTION
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.

2np5__assembly_2__model_1

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

Download this curve (.dat)

2np5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2np5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.33 Å
Rg (electron density)	20.09 Å
Total Rg	21.00 Å
Atom count	2592
Residues	337
Excluded volume	46810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2np5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2np5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2np5__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Transcriptional regulator
Molecular weight formula_weight	21828.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5881

MRERRYSSTSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEMFAFALRTLVDKLLARLSEVERGGDPARALFAAMSQLLPLDEARSREAHVMAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGMILQGADVVPSSSIELAS

Source Source

Source organism organism	Rhodococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	101510
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ETHYL DIMETHYL AMMONIO PROPANE SULFONATE
Molecular weight formula_weight	195.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	421

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2np5a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d2np5a2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d2np5b1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d2np5b2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d2np5c1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d2np5c2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

Domain ID domain_id	d2np5d1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.9 — Tetracyclin repressor-like, N-terminal domain

Domain ID domain_id	d2np5d2
Class class	a — All alpha proteins
Fold Fold fold	a.121 — Tetracyclin repressor-like, C-terminal domain
Superfamily Superfamily superfamily	a.121.1 — Tetracyclin repressor-like, C-terminal domain
Family Family family	a.121.1.1 — Tetracyclin repressor-like, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	2np5A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	2np5B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	2np5C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

Domain ID domain_id	2np5D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	357 — Tetracycline Repressor; domain 2
Homologous superfamily homologous superfamily	10 — Tetracycline Repressor, domain 2

▶

Unit-cell length a length_a	50.721 Å
Unit-cell length b length_b	52.230 Å
Unit-cell length c length_c	72.853 Å
Unit-cell angle α angle_alpha	102.31 °
Unit-cell angle β angle_beta	107.25 °
Unit-cell angle γ angle_gamma	89.71 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.800 Å
R factor r_factor	0.1788
R_work r_work	0.1766
R_free r_free	0.2195

Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.

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

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

2np5__assembly_2__model_1

2np5__assembly_2__model_1 | I(q)

2np5__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a transcriptional regulator (RHA1_ro04179) from Rhodococcus sp. Rha1.

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

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

2np5__assembly_2__model_1

2np5__assembly_2__model_1 | I(q)

2np5__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 (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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)