SAXSdb — 1rty

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

yvqk protein

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	PHOSPHATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O34899_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–193； UniProt 2–193 Author chain B； PDBConstruct 2–193； UniProt 2–193 Author chain C； PDBConstruct 2–193； UniProt 2–193

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	1rty
Deposition date deposition_date	2003-12-10
Structure title title	Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128
Keywords keywords	;all alpha-helical trimeric protein, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

1rty__assembly_1__model_1

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

Download this curve (.dat)

1rty__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rty__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.78 Å
Rg (electron density)	21.59 Å
Total Rg	22.47 Å
Atom count	3809
Residues	479
Excluded volume	67757 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rty__assembly_1__model_1`	trimeric （3）	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	yvqk protein
Molecular weight formula_weight	21613.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3992

MKLYTKTGDKGQTGLVGGRTDKDSLRVESYGTIDELNSFIGLALAELSGQPGFEDLTAELLTIQHELFDCGGDLAIVTERKDYKLTEESVSFLETRIDAYTAEAPELKKFILPGGSKCASLLHIARTITRRAERRVVALMKSEEIHETVLRYLNRLSDYFFAGARVVNARSGIGDVEYERSAIVFRDRNSSES

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	183

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1rtya_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.2 — Cobalamin adenosyltransferase-like
Family Family family	a.25.2.2 — Cobalamin adenosyltransferase

Domain ID domain_id	d1rtyb_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.2 — Cobalamin adenosyltransferase-like
Family Family family	a.25.2.2 — Cobalamin adenosyltransferase

Domain ID domain_id	d1rtyc_
Class class	a — All alpha proteins
Fold Fold fold	a.25 — Ferritin-like
Superfamily Superfamily superfamily	a.25.2 — Cobalamin adenosyltransferase-like
Family Family family	a.25.2.2 — Cobalamin adenosyltransferase

CATH v4.4 (3 domains)

Domain ID domain_id	1rtyA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	1rtyB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

Domain ID domain_id	1rtyC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1200 — Hypothetical Protein Ta1238; Chain: A;
Homologous superfamily homologous superfamily	10 — Cobalamin adenosyltransferase-like

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Unit-cell length a length_a	104.350 Å
Unit-cell length b length_b	104.350 Å
Unit-cell length c length_c	55.985 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	12

Space group space_group	P 4
Space-group number int_tables_number	75
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	24.600 Å
R factor r_factor	0.2250
R_work r_work	0.2240
R_free r_free	0.2800

Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128

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

yvqk 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

1rty__assembly_1__model_1

1rty__assembly_1__model_1 | I(q)

1rty__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 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of Bacillus subtilis YvqK, a putative ATP-binding Cobalamin Adenosyltransferase, The North East Structural Genomics Target SR128

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

yvqk 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

1rty__assembly_1__model_1

1rty__assembly_1__model_1 | I(q)

1rty__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 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)