SAXSdb — 2rbf

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

Bifunctional protein putA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(DTPDTDTPDGPDCPDGPDGPDTPDTPDGPDCPDAPDCPDCPDTPDTPDTPDCPDAPDAPDA)-3') ; × 1 ;DNA (5'-D(DTPDTPDTPDGPDAPDAPDAPDGPDGPDTPDGPDCPDAPDAPDCPDCPDGPDCPDAPDAPDA)-3') ; × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PUTA_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 3–54； UniProt 1–52 Author chain B； PDBConstruct 3–54； UniProt 1–52

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	2rbf
Deposition date deposition_date	2007-09-18
Structure title title	Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)
Keywords keywords	;Protein-DNA complex, ribbon-helix-helix, proline utilization A, PutA, DNA-binding, FAD, Flavoprotein, Multifunctional enzyme, NAD, Oxidoreductase, Proline metabolism, Repressor, Transcription, Transcription regulation, OXIDOREDUCTASE-DNA COMPLEX ;; OXIDOREDUCTASE/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.

2rbf__assembly_1__model_1

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

Download this curve (.dat)

2rbf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rbf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.40 Å
Rg (electron density)	18.26 Å
Total Rg	19.03 Å
Atom count	1466
Residues	127
Excluded volume	23636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rbf__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DTPDTDTPDGPDCPDGPDGPDTPDTPDGPDCPDAPDCPDCPDTPDTPDTPDCPDAPDAP*DA)-3') ;
Molecular weight formula_weight	6404.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	1493

TTTGCGGTTGCACCTTTCAAA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DTPDTPDTPDGPDAPDAPDAPDGPDGPDTPDGPDCPDAPDAPDCPDCPDGPDCPDAPDAP*DA)-3') ;
Molecular weight formula_weight	6480.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TTTGAAAGGTGCAACCGCAAA

Entity 3 Entity 3 polymer

Description description	Bifunctional protein putA
Molecular weight formula_weight	6152.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

GHMGTTTMGVKLDDATRERIKSAATRIDRTPHWLIKQAIFSYLEQLENSDTLPE

Source Source

Source organism organism	Escherichia coli
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2rbfa_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.11 — PutA pre-N-terminal region-like

Domain ID domain_id	d2rbfb_
Class class	a — All alpha proteins
Fold Fold fold	a.43 — Ribbon-helix-helix
Superfamily Superfamily superfamily	a.43.1 — Ribbon-helix-helix
Family Family family	a.43.1.11 — PutA pre-N-terminal region-like

CATH v4.4 (2 domains)

Domain ID domain_id	2rbfA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

Domain ID domain_id	2rbfB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1220 — Arc Repressor Mutant
Homologous superfamily homologous superfamily	10 — Met repressor-like

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Unit-cell length a length_a	90.911 Å
Unit-cell length b length_b	44.084 Å
Unit-cell length c length_c	55.230 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.50 °
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	2.250 Å
Low-resolution limit resolution_low	54.150 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2460

Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)

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

Bifunctional protein putA

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

2rbf__assembly_1__model_1

2rbf__assembly_1__model_1 | I(q)

2rbf__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)

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

Bifunctional protein putA

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

2rbf__assembly_1__model_1

2rbf__assembly_1__model_1 | I(q)

2rbf__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)