SAXSdb — 1ynb

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

hypothetical protein AF1432

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28840_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 1–173 Author chain B； PDBConstruct 1–173； UniProt 1–173 Author chain C； PDBConstruct 1–173； UniProt 1–173

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	1ynb
Deposition date deposition_date	2005-01-24
Structure title title	crystal structure of genomics APC5600
Keywords keywords	Structural Genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, Sulfur SAD, HYDROLASE; HYDROLASE
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.

1ynb__assembly_1__model_1

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

Download this curve (.dat)

1ynb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ynb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.34 Å
Rg (electron density)	24.42 Å
Total Rg	25.35 Å
Atom count	4023
Residues	501
Excluded volume	71577 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ynb__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ynb__assembly_2__model_1`	hexameric （6）	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) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ynba1
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d1ynbb_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d1ynbc_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

CATH v4.4 (3 domains)

Domain ID domain_id	1ynbA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	1ynbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	1ynbC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

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Unit-cell length a length_a	85.320 Å
Unit-cell length b length_b	131.410 Å
Unit-cell length c length_c	58.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	28.360 Å
R factor r_factor	0.2060
R_work r_work	0.2060
R_free r_free	0.2430

Description description	hypothetical protein AF1432
Molecular weight formula_weight	19847.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4303

crystal structure of genomics APC5600

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

hypothetical protein AF1432

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

1ynb__assembly_1__model_1

1ynb__assembly_1__model_1 | I(q)

1ynb__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	224325
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	280

crystal structure of genomics APC5600

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

hypothetical protein AF1432

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

1ynb__assembly_1__model_1

1ynb__assembly_1__model_1 | I(q)

1ynb__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) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)