SAXSdb — 2ikk

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

Hypothetical transcriptional regulator yurK

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	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	YURK_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–173； UniProt 94–242 Author chain B； PDBConstruct 25–173； UniProt 94–242

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	2ikk
Deposition date deposition_date	2006-10-02
Structure title title	Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168
Keywords keywords	;APC85442, Yurk, bacillus subtilis subsp. subtilis str. 168, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2ikk__assembly_1__model_1

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

Download this curve (.dat)

2ikk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ikk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.14 Å
Rg (electron density)	22.46 Å
Total Rg	23.18 Å
Atom count	2369
Residues	287
Excluded volume	42322 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ikk__assembly_1__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	Hypothetical transcriptional regulator yurK
Molecular weight formula_weight	19893.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2548

MHHHHHHSSGVDLGTENLYFQSNASTGKKPKHHVLSHDIIPASKPIAEKLQIQPESPVVELKRILYNDDQPLTFEVTHYPLDLFPGIDTFIADGVSMHDILKQQYKVVPTHNTKLLNVVYAQQEESKYLDCDIGDALFEIDKTAFTSNDQPIYCSLFLMHTNRVTFTINSPYT

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21

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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ikka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.190 — Chorismate lyase-like
Superfamily Superfamily superfamily	d.190.1 — Chorismate lyase-like
Family Family family	d.190.1.2 — UTRA domain

Domain ID domain_id	d2ikka2
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	d2ikkb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.190 — Chorismate lyase-like
Superfamily Superfamily superfamily	d.190.1 — Chorismate lyase-like
Family Family family	d.190.1.2 — UTRA domain

Domain ID domain_id	d2ikkb3
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 (2 domains)

Domain ID domain_id	2ikkA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1410 — Chorismate lyase
Homologous superfamily homologous superfamily	10 — Chorismate lyase-like

Domain ID domain_id	2ikkB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1410 — Chorismate lyase
Homologous superfamily homologous superfamily	10 — Chorismate lyase-like

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Unit-cell length a length_a	40.509 Å
Unit-cell length b length_b	104.704 Å
Unit-cell length c length_c	40.538 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.58 °
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	1.800 Å
Low-resolution limit resolution_low	35.600 Å
R factor r_factor	0.1961
R_work r_work	0.1943
R_free r_free	0.2303

Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168

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

Hypothetical transcriptional regulator yurK

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

2ikk__assembly_1__model_1

2ikk__assembly_1__model_1 | I(q)

2ikk__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus subtilis subsp. subtilis str. 168

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

Hypothetical transcriptional regulator yurK

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

2ikk__assembly_1__model_1

2ikk__assembly_1__model_1 | I(q)

2ikk__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)