1tjl

Crystal structure of transcription factor DksA from E. coli

Method: X-RAY DIFFRACTION

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

DnaK suppressor protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
11	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DKSA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–151； UniProt 1–151 Author chain B； PDBConstruct 1–151； UniProt 1–151 Author chain C； PDBConstruct 1–151； UniProt 1–151 Author chain D； PDBConstruct 1–151； UniProt 1–151 Author chain E； PDBConstruct 1–151； UniProt 1–151 Author chain F； PDBConstruct 1–151； UniProt 1–151 Author chain G； PDBConstruct 1–151； UniProt 1–151 Author chain H； PDBConstruct 1–151； UniProt 1–151 Author chain I； PDBConstruct 1–151； UniProt 1–151 Author chain J； PDBConstruct 1–151； UniProt 1–151

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	1tjl
Deposition date deposition_date	2004-06-06
Structure title title	Crystal structure of transcription factor DksA from E. coli
Keywords keywords	;DksA, transcription factor, RNA polymerase, stringent response, ppGpp, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, TRANSCRIPTION ;; TRANSCRIPTION
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.

1tjl__assembly_9__model_1

Assembly 9 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1tjl__assembly_9__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tjl__assembly_9__model_1 | P(r) · Pending

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

Rg（Guinier）	20.50 Å
Rg (electron density)	19.70 Å
Total Rg	20.33 Å
Atom count	1180
Residues	145
Excluded volume	20772 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tjl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tjl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tjl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1tjl__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1tjl__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1tjl__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1tjl__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1tjl__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1tjl__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1tjl__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`1tjl__assembly_11__model_1`	dimeric （2）	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	DnaK suppressor protein
Molecular weight formula_weight	17554.8 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	12822

MQEGQNRKTSSLSILAIAGVEPYQEKPGEEYMNEAQLAHFRRILEAWRNQLRDEVDRTVTHMQDEAANFPDPVDRAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIREKQMAG

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1022

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1tjla1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjla2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlb1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlb2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlc1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlc2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjld1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjld2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjle1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjle2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlf1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlf2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlg1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlg2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlh1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlh2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjli1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjli2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

Domain ID domain_id	d1tjlj1
Class class	a — All alpha proteins
Fold Fold fold	a.2 — Long alpha-hairpin
Superfamily Superfamily superfamily	a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain
Family Family family	a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain

Domain ID domain_id	d1tjlj2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger

CATH v4.4 (10 domains)

Domain ID domain_id	1tjlA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlF00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlH00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

Domain ID domain_id	1tjlJ00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	910 — DksA, coiled-coil domain

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Unit-cell length a length_a	91.319 Å
Unit-cell length b length_b	96.593 Å
Unit-cell length c length_c	117.477 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	20

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	38.950 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2680

Crystal structure of transcription factor DksA from E. coli

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

DnaK suppressor protein

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

1tjl__assembly_9__model_1

1tjl__assembly_9__model_1 | I(q)

1tjl__assembly_9__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of transcription factor DksA from E. coli

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

DnaK suppressor protein

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

1tjl__assembly_9__model_1

1tjl__assembly_9__model_1 | I(q)

1tjl__assembly_9__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)