1to0

X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis

Method: X-RAY DIFFRACTION

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

Hypothetical UPF0247 protein yyda

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	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YYDA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159 Author chain B； PDBConstruct 1–159； UniProt 1–159 Author chain C； PDBConstruct 1–159； UniProt 1–159 Author chain D； PDBConstruct 1–159； UniProt 1–159 Author chain E； PDBConstruct 1–159； UniProt 1–159 Author chain F； PDBConstruct 1–159； UniProt 1–159 Author chain G； PDBConstruct 1–159； UniProt 1–159 Author chain H； PDBConstruct 1–159； UniProt 1–159

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	1to0
Deposition date deposition_date	2004-06-11
Structure title title	X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis
Keywords keywords	STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG; 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.

1to0__assembly_1__model_1

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

Download this curve (.dat)

1to0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1to0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.05 Å
Rg (electron density)	19.91 Å
Total Rg	20.87 Å
Atom count	2359
Residues	284
Excluded volume	43138 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1to0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1to0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1to0__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1to0__assembly_4__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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1to0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

Domain ID domain_id	d1to0h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.3 — YbeA-like

CATH v4.4 (8 domains)

Domain ID domain_id	1to0A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

Domain ID domain_id	1to0H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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Unit-cell length a length_a	98.691 Å
Unit-cell length b length_b	70.553 Å
Unit-cell length c length_c	100.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2900

Description description	Hypothetical UPF0247 protein yyda
Molecular weight formula_weight	19455.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	9527

X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis

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

Hypothetical UPF0247 protein yyda

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

1to0__assembly_1__model_1

1to0__assembly_1__model_1 | I(q)

1to0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

X-ray structure of Northeast Structural Genomics target protein sr145 from Bacillus subtilis

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

Hypothetical UPF0247 protein yyda

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

1to0__assembly_1__model_1

1to0__assembly_1__model_1 | I(q)

1to0__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)