SAXSdb — 1yga

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

Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region

Saccharomyces cerevisiae

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	YN9A_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–342； UniProt 1–342 Author chain B； PDBConstruct 1–342； UniProt 1–342

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	1yga
Deposition date deposition_date	2005-01-04
Structure title title	CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
Keywords keywords	;ALDOSE_1_EPIMERASE, SUGAR METABOLISM, PREDICTED, STRUCTURAL GENOMICS, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, ISOMERASE ;; ISOMERASE
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.

1yga__assembly_1__model_1

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

Download this curve (.dat)

1yga__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yga__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.30 Å
Rg (electron density)	26.65 Å
Total Rg	27.49 Å
Atom count	5244
Residues	672
Excluded volume	93149 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yga__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)

Entity 1 Entity 1 polymer

Description description	Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region
Molecular weight formula_weight	37896.6 kDa
EC 编号 ec_number	5.1.3.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5783

MSNSNGDNKYGVITIGDEKKFQATIAPLGATLVDLKVNGQSVVQGYSNVQDYLTDGNMMGATVGRYANRIAKGVFSLDDGPHKLTVNNCGNTNHSSISSLNLKQYKASPVENPSKGVYVVEFKLLDDHTQPNPNEFPGDLEVTVKYTLNVAEMTLDMEYQAQLVRGDATPINMTNHSYFNLNKVKSEKSIRGTEVKVCSNKSLEVTEGALLPTGKIIERNIATFDSTKPTVLHEDTPVFDCTFIIDANKDLKTTDSVSVNKLVPVFKAYHPESHIKFEVSTTEPTVHLYTGDNLCGKFVPRSGFAVQQGRYVDAINRDEWRGCVLLKRGEVYTSKTQYKFDI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	539

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ygaa_
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.0 — automated matches

Domain ID domain_id	d1ygab_
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.5 — Galactose mutarotase-like
Family Family family	b.30.5.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	1ygaA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1ygaB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	78.860 Å
Unit-cell length b length_b	88.070 Å
Unit-cell length c length_c	103.080 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	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2290

CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

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

Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region

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

1yga__assembly_1__model_1

1yga__assembly_1__model_1 | I(q)

1yga__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)

CRYSTAL STRUCTURE OF Saccharomyces cerevisiae YN9A PROTEIN, NEW YORK STRUCTURAL GENOMICS CONSORTIUM

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

Hypothetical 37.9 kDa protein in BIO3-HXT17 intergenic region

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

1yga__assembly_1__model_1

1yga__assembly_1__model_1 | I(q)

1yga__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)