SAXSdb — 2pih

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

Protein ymcA

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YMCA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 1–143 Author chain B； PDBConstruct 1–143； UniProt 1–143

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	2pih
Deposition date deposition_date	2007-04-13
Structure title title	Crystal structure of Protein ymcA from Bacillus subtilis, NorthEast Structural Genomics target SR375
Keywords keywords	;ymcA, regulate community development, Structural Genomics, PSI-2, 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.

2pih__assembly_1__model_1

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

Download this curve (.dat)

2pih__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pih__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.24 Å
Rg (electron density)	26.76 Å
Total Rg	27.37 Å
Atom count	1972
Residues	242
Excluded volume	35065 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pih__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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2piha1
Class class	a — All alpha proteins
Fold Fold fold	a.281 — YheA-like
Superfamily Superfamily superfamily	a.281.1 — YheA/YmcA-like
Family Family family	a.281.1.1 — YmcA-like

Domain ID domain_id	d2pihb_
Class class	a — All alpha proteins
Fold Fold fold	a.281 — YheA-like
Superfamily Superfamily superfamily	a.281.1 — YheA/YmcA-like
Family Family family	a.281.1.1 — YmcA-like

CATH v4.4 (2 domains)

Domain ID domain_id	2pihA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	10 — YheA/YmcA-like

Domain ID domain_id	2pihB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1500 — YheA-like fold
Homologous superfamily homologous superfamily	10 — YheA/YmcA-like

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Unit-cell length a length_a	29.322 Å
Unit-cell length b length_b	52.201 Å
Unit-cell length c length_c	55.448 Å
Unit-cell angle α angle_alpha	61.85 °
Unit-cell angle β angle_beta	90.64 °
Unit-cell angle γ angle_gamma	90.01 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2540

Description description	Protein ymcA
Molecular weight formula_weight	17399.1 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	2179

Crystal structure of Protein ymcA from Bacillus subtilis, NorthEast Structural Genomics target SR375

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

Protein ymcA

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

2pih__assembly_1__model_1

2pih__assembly_1__model_1 | I(q)

2pih__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
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	207

Crystal structure of Protein ymcA from Bacillus subtilis, NorthEast Structural Genomics target SR375

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

Protein ymcA

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

2pih__assembly_1__model_1

2pih__assembly_1__model_1 | I(q)

2pih__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)