1y7p

1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus fulgidus, Probable Metabolic Regulator

Method: X-RAY DIFFRACTION

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

Hypothetical protein AF1403

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	beta-D-ribopyranose × 2 ZINC ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	beta-D-ribopyranose × 2 ZINC ION × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	beta-D-ribopyranose × 6 ZINC ION × 6 water × 6	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	beta-D-ribopyranose × 3 ZINC ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1403_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–221； UniProt 1–219 Author chain B； PDBConstruct 3–221； UniProt 1–219 Author chain C； PDBConstruct 3–221； UniProt 1–219

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	1y7p
Deposition date deposition_date	2004-12-09
Structure title title	1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus fulgidus, Probable Metabolic Regulator
Keywords keywords	;Structural Genomics, Protein structure initiative, PSI, Archaeoglobus fulgidus, alpha-beta-alpha sandwich, Midwest Center for Structural Genomics, MCSG, 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.

1y7p__assembly_1__model_1

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

Download this curve (.dat)

1y7p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y7p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.16 Å
Rg (electron density)	21.13 Å
Total Rg	22.11 Å
Atom count	3250
Residues	418
Excluded volume	58731 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y7p__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1y7p__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1y7p__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1y7p__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein AF1403
Molecular weight formula_weight	24454.4 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	5163

GHMLRGLRIIAENKIGVLRDLTTIIAEEGGNITFAQTFLIKHGEHEGKALIYFEIEGGDFEKILERVKTFDYIIEIEEEESFERVFGKRVIILGGGALVSQVAIGAISEADRHNLRGERISVDTMPVVGEEEIAEAVKAVSRLHRAEVLVLAGGIMGGKITEEVKKLRKSGIRVISLSMFGSVPDVADVVISDPVMAGTLAVMHISEKAKFDLDRVKGRRIGK

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	beta-D-ribopyranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1y7pa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.7 — AF1403 C-terminal domain-like

Domain ID domain_id	d1y7pa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.12 — AF1403 N-terminal domain-like

Domain ID domain_id	d1y7pb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.7 — AF1403 C-terminal domain-like

Domain ID domain_id	d1y7pb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.12 — AF1403 N-terminal domain-like

Domain ID domain_id	d1y7pb3
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	d1y7pc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.7 — AF1403 C-terminal domain-like

Domain ID domain_id	d1y7pc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.18 — ACT-like
Family Family family	d.58.18.12 — AF1403 N-terminal domain-like

Domain ID domain_id	d1y7pc3
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

CATH v4.4 (6 domains)

Domain ID domain_id	1y7pA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	1y7pA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10550 — Hypothetical protein af1403; domain 2

Domain ID domain_id	1y7pB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	1y7pB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10550 — Hypothetical protein af1403; domain 2

Domain ID domain_id	1y7pC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	260 — ACT domain

Domain ID domain_id	1y7pC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10550 — Hypothetical protein af1403; domain 2

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Unit-cell length a length_a	95.709 Å
Unit-cell length b length_b	95.709 Å
Unit-cell length c length_c	167.551 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	36.340 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2550

1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus fulgidus, Probable Metabolic Regulator

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

Hypothetical protein AF1403

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

1y7p__assembly_1__model_1

1y7p__assembly_1__model_1 | I(q)

1y7p__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

1.9 A Crystal Structure of a Protein of Unknown Function AF1403 from Archaeoglobus fulgidus, Probable Metabolic Regulator

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

Hypothetical protein AF1403

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

1y7p__assembly_1__model_1

1y7p__assembly_1__model_1 | I(q)

1y7p__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)