SAXSdb — 2icu

▼

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

Hypothetical protein yedK

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	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YEDK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–229； UniProt 1–222 Author chain B； PDBConstruct 8–229； UniProt 1–222

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2icu
Deposition date deposition_date	2006-09-13
Structure title title	Crystal Structure of Hypothetical Protein YedK From Escherichia coli
Keywords keywords	;HYPOTHETICAL PROTEIN YEDK, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE INITIATIVE, SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS, SECSG, RIKEN, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2icu__assembly_2__model_1

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

Download this curve (.dat)

2icu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2icu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.52 Å
Rg (electron density)	16.28 Å
Total Rg	17.27 Å
Atom count	1659
Residues	210
Excluded volume	29302 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2icu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2icu__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2icua_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.303 — BB1717-like
Superfamily Superfamily superfamily	d.303.1 — BB1717-like
Family Family family	d.303.1.0 — automated matches

Domain ID domain_id	d2icub_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.303 — BB1717-like
Superfamily Superfamily superfamily	d.303.1 — BB1717-like
Family Family family	d.303.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2icuA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1680 — hypothetical protein yedk fold
Homologous superfamily homologous superfamily	10 — SOS response associated peptidase-like

Domain ID domain_id	2icuB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1680 — hypothetical protein yedk fold
Homologous superfamily homologous superfamily	10 — SOS response associated peptidase-like

▶

Unit-cell length a length_a	46.687 Å
Unit-cell length b length_b	67.366 Å
Unit-cell length c length_c	75.125 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	18.590 Å
R factor r_factor	0.1742
R_work r_work	0.1726
R_free r_free	0.2032

Description description	Hypothetical protein yedK
Molecular weight formula_weight	25715.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4066

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

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

Hypothetical protein yedK

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

2icu__assembly_2__model_1

2icu__assembly_2__model_1 | I(q)

2icu__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	749

Crystal Structure of Hypothetical Protein YedK From Escherichia coli

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

Hypothetical protein yedK

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

2icu__assembly_2__model_1

2icu__assembly_2__model_1 | I(q)

2icu__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)