1d5y

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

Method: X-RAY DIFFRACTION D_max: 153.4 Å Quality: GOOD

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 3–289 Chain B； UniProt 3–289	Fragment：RESIDUES 3-289, KLAAA EXTENSION AFTER RESIDUE 289	;DNA (5'-D(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAPG)-3') ; × 1 ;DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTPC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Peg 8000, MES, MgCl2, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.302
2	Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain C； UniProt 3–289 Chain D； UniProt 3–289	Fragment：RESIDUES 3-289, KLAAA EXTENSION AFTER RESIDUE 289	;DNA (5'-D(TPGPAPCPAPGPCPAPCPTPGPAPAPTPGPTPCPAPAPAPG)-3') ; × 1 ;DNA (5'-D(APCPTPTPTPGPAPCPAPTPTPCPAPGPTPGPCPTPGPTPC)-3') ; × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Peg 8000, MES, MgCl2, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.70 Å R-free 0.302

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1D5Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VWY Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation Deposited 2021-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain G 1–289（289 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.57 Å
7VWZ Cryo-EM structure of Rob-dependent transcription activation complex in a unique conformation Deposited 2021-11-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–289（289 aa） Chain I 1–289（289 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.17 Å
Radius of gyration Rg (electron density) rg_electron	47.20 Å
Forward intensity I(0) i0	439645000.00
Molecular weight molecular_weight	157230.0 kDa
Excluded volume excluded_volume	190060 Å³
Envelope volume envelope_volume	303730 Å³
Hydration-shell volume shell_volume	54985 Å³
Envelope diameter envelope_diameter	162.6 Å
Shell Rg shell_rg	50.55 Å
Envelope Rg envelope_rg	45.34 Å
Shape Rg shape_rg	47.28 Å
Total Rg total_rg	47.08 Å
Total atoms total_atoms	10986
Residues n_residues	1236
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	153.4 Å
Rg (real space) rg_real	46.16 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	4.3960e+08
I(0) uncertainty (real space) i0_real_error	8.5370e+06
Rg (reciprocal space) rg_reciprocal	46.17 Å
I(0) (reciprocal space) i0_reciprocal	439600000.0000
Solution quality estimate total_estimate	0.8798
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	58.6 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.380
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12090000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.832

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/d5/1d5y/1d5y.fit
pddf	/app/data/pr_computation/d5/1d5y/1d5y.pr.out
profile	/app/data/saxs_computation/d5/1d5y/1d5y.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. 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

来源 Source

7. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (16 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)