SAXSdb — 1ysp

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

Transcriptional regulator kdgR

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	SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDGR_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–179； UniProt 88–263

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	1ysp
Deposition date deposition_date	2005-02-08
Structure title title	Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR.
Keywords keywords	;transcriptional regulator, KdgR, IclR, Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, 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.

1ysp__assembly_1__model_1

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

Download this curve (.dat)

1ysp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ysp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.67 Å
Rg (electron density)	15.23 Å
Total Rg	16.40 Å
Atom count	1319
Residues	164
Excluded volume	23453 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ysp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ysp__assembly_2__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	Transcriptional regulator kdgR
Molecular weight formula_weight	20842.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1535

GHMDLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDSMYNLRMYSRIGRRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSISFPTLRFSEERLQEYVAMLHTAARKISAQMGYHDYPFGS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1yspa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.110 — Profilin-like
Superfamily Superfamily superfamily	d.110.2 — GAF domain-like
Family Family family	d.110.2.0 — automated matches

Domain ID domain_id	d1yspa2
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 (1 domains)

Domain ID domain_id	1yspA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	40 — GAF domain

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Unit-cell length a length_a	153.540 Å
Unit-cell length b length_b	31.540 Å
Unit-cell length c length_c	37.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	76.700 Å
R factor r_factor	0.2143
R_work r_work	0.2118
R_free r_free	0.2586

Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR.

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

Transcriptional regulator kdgR

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

1ysp__assembly_1__model_1

1ysp__assembly_1__model_1 | I(q)

1ysp__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 (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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the C-terminal domain of E. coli transcriptional regulator KdgR.

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

Transcriptional regulator kdgR

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

1ysp__assembly_1__model_1

1ysp__assembly_1__model_1 | I(q)

1ysp__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 (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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)