SAXSdb — 1ym5

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

Hypothetical 32.6 kDa protein in DAP2-SLT2 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	YHI9_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 1–294

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	1ym5
Deposition date deposition_date	2005-01-20
Structure title title	Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
Keywords keywords	PhzF enzyme superfamily, double hot-dog, Structural Genomics, Paris-Sud Yeast Structural Genomics, YSG, Oxidoreductase; OXIDOREDUCTASE
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.

1ym5__assembly_1__model_1

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

Download this curve (.dat)

1ym5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ym5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.74 Å
Rg (electron density)	25.77 Å
Total Rg	26.71 Å
Atom count	4584
Residues	588
Excluded volume	82404 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ym5__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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	1ym5A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	1ym5A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

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Unit-cell length a length_a	81.188 Å
Unit-cell length b length_b	81.188 Å
Unit-cell length c length_c	98.146 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1908
R_work r_work	0.1876
R_free r_free	0.2511

Description description	Hypothetical 32.6 kDa protein in DAP2-SLT2 intergenic region
Molecular weight formula_weight	33427.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2446

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

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

Hypothetical 32.6 kDa protein in DAP2-SLT2 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

1ym5__assembly_1__model_1

1ym5__assembly_1__model_1 | I(q)

1ym5__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

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

Hypothetical 32.6 kDa protein in DAP2-SLT2 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

1ym5__assembly_1__model_1

1ym5__assembly_1__model_1 | I(q)

1ym5__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)