1d5y

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA

Method: X-RAY DIFFRACTION

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

ROB TRANSCRIPTION FACTOR

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(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAPG)-3') ; × 1 ;DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTPC)-3') ; × 1	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAPG)-3') ; × 1 ;DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTPC)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ROB_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–287； UniProt 3–289 Author chain B； PDBConstruct 1–287； UniProt 3–289 Author chain C； PDBConstruct 1–287； UniProt 3–289 Author chain D； PDBConstruct 1–287； UniProt 3–289

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	1d5y
Deposition date deposition_date	1999-10-12
Structure title title	CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA
Keywords keywords	Protein-DNA complex, Rob Transcription factor, DNA, transcription-DNA COMPLEX; transcription/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.

1d5y__assembly_2__model_1

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

Download this curve (.dat)

1d5y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1d5y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	37.83 Å
Rg (electron density)	39.88 Å
Total Rg	39.59 Å
Atom count	5493
Residues	618
Excluded volume	95029 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1d5y__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1d5y__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAP*G)-3') ;
Molecular weight formula_weight	6480.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,O
Atom count atom_count	10986

TGACAGCACTGAATGTCAAAG

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTP*C)-3') ;
Molecular weight formula_weight	6404.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N,P

ACTTTGACATTCAGTGCTGTC

Entity 3 Entity 3 polymer

Description description	ROB TRANSCRIPTION FACTOR
Molecular weight formula_weight	33394.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

QAGIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSPEWSAFGIRPPLRLGEFTMPEHKFVTLEDTPLIGVTQSYSCSLEQISDFRHEMRYQFWHDFLGNAPTIPPVLYGLNETRPSQDKDDEQEVFYTTALAQDQADGYVLTGHPVMLQGGEYVMFTYEGLGTGVQEFILTVYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPINLRCELLIPIRRKLAAA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1d5ya1
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5ya2
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5ya3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.2 — Rob transcription factor, C-terminal domain

Domain ID domain_id	d1d5ya4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1d5yb1
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yb2
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.2 — Rob transcription factor, C-terminal domain

Domain ID domain_id	d1d5yb4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1d5yc1
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yc2
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.2 — Rob transcription factor, C-terminal domain

Domain ID domain_id	d1d5yc4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1d5yd1
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yd2
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.4.1.8 — AraC type transcriptional activator

Domain ID domain_id	d1d5yd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.60 — Probable bacterial effector-binding domain
Superfamily Superfamily superfamily	d.60.1 — Probable bacterial effector-binding domain
Family Family family	d.60.1.2 — Rob transcription factor, C-terminal domain

Domain ID domain_id	d1d5yd4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (12 domains)

Domain ID domain_id	1d5yA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yA03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	1d5yB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yB03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	1d5yC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yC03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

Domain ID domain_id	1d5yD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1d5yD03
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	80 — Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A
Homologous superfamily homologous superfamily	10 — Regulatory factor, effector binding domain

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Unit-cell length a length_a	75.384 Å
Unit-cell length b length_b	208.012 Å
Unit-cell length c length_c	67.731 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2540
R_work r_work	0.2540
R_free r_free	0.3020

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA

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

ROB TRANSCRIPTION FACTOR

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

1d5y__assembly_2__model_1

1d5y__assembly_2__model_1 | I(q)

1d5y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

CATH v4.4 (12 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE E. COLI ROB TRANSCRIPTION FACTOR IN COMPLEX WITH DNA

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

ROB TRANSCRIPTION FACTOR

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

1d5y__assembly_2__model_1

1d5y__assembly_2__model_1 | I(q)

1d5y__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

CATH v4.4 (12 domains)

7. Citations (1)