SAXSdb — 2nyg

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

YokD protein

Bacillus subtilis

UniProt O32003

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COENZYME A × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COENZYME A × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	COENZYME A × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O32003_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–273； UniProt 2–272 Author chain B； PDBConstruct 3–273； UniProt 2–272 Author chain C； PDBConstruct 3–273； UniProt 2–272 Author chain D； PDBConstruct 3–273； UniProt 2–272 Author chain E； PDBConstruct 3–273； UniProt 2–272 Author chain F； PDBConstruct 3–273； UniProt 2–272

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	2nyg
Deposition date deposition_date	2006-11-20
Structure title title	Crystal structure of YokD protein from Bacillus subtilis
Keywords keywords	;pfam02522, NYSGXRC, 10116c, Aminoglycoside 3-N-acetyltransferase, PSI-2, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, 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.

2nyg__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2nyg__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nyg__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	24.79 Å
Total Rg	25.47 Å
Atom count	3889
Residues	508
Excluded volume	69056 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nyg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nyg__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nyg__assembly_3__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	YokD protein
Molecular weight formula_weight	31022.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	12534

SLKKIVESTTFPRTKQSITEDLKALGLKKGMTVLVHSSLSSIGWVNGGAVAVIQALIDVVTEEGTIVMPSQSVELSDPKEWGNPPVPEEWWDIIRESMPAYNSNYTPTTRGMGQIVELFRSYPEVKRSNHPNYSFVAWGKHKNKILNQHPLEFGLGEQSPLGKLYIRESYVLLLGADFDSSTCFHLAEYRIPYQKIINRGAPIIVEGKRVWKEYKELEFREELFQEVGQAFEAEHNMKVGKVGSANCRLFSLTEAVDFAEKWFINNDSKNIKK

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	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d2nyga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

Domain ID domain_id	d2nyga2
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	d2nygb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

Domain ID domain_id	d2nygc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

Domain ID domain_id	d2nygc3
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	d2nygd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

Domain ID domain_id	d2nygd3
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	d2nyge_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

Domain ID domain_id	d2nygf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.140 — TTHA0583/YokD-like
Superfamily Superfamily superfamily	c.140.1 — TTHA0583/YokD-like
Family Family family	c.140.1.2 — Aminoglycoside 3-N-acetyltransferase-like

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Unit-cell length a length_a	73.020 Å
Unit-cell length b length_b	132.390 Å
Unit-cell length c length_c	185.800 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	49.040 Å
R factor r_factor	0.2570
R_work r_work	0.2570
R_free r_free	0.2960

Crystal structure of YokD protein from Bacillus subtilis

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

YokD 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

2nyg__assembly_3__model_1

2nyg__assembly_3__model_1 | I(q)

2nyg__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 9 domains

SCOP 2.08 (9 domains)

7. Citations (1)

Crystal structure of YokD protein from Bacillus subtilis

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

YokD 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

2nyg__assembly_3__model_1

2nyg__assembly_3__model_1 | I(q)

2nyg__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 9 domains

SCOP 2.08 (9 domains)

7. Citations (1)