SAXSdb — 1gyy

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

HYPOTHETICAL PROTEIN YDCE

ESCHERICHIA COLI

UniProt P31992

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDCE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 2–77 Author chain B； PDBConstruct 1–76； UniProt 2–77

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	1gyy
Deposition date deposition_date	2002-04-30
Structure title title	The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity
Keywords keywords	TAUTOMERASE, ISOMERASE, HYPOTHETICAL PROTEIN, COMPLETE PROTE; 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.

1gyy__assembly_1__model_1

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

Download this curve (.dat)

1gyy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gyy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.37 Å
Rg (electron density)	14.86 Å
Total Rg	15.99 Å
Atom count	1214
Residues	152
Excluded volume	21652 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gyy__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 (3)

Entity 1 Entity 1 polymer

Description description	HYPOTHETICAL PROTEIN YDCE
Molecular weight formula_weight	8550.7 kDa
EC 编号 ec_number	5.3.2.1
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	1556

PHIDIKCFPRELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWDAEIAPQMEALIKKPGYSMNA

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE
Molecular weight formula_weight	181.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	283

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gyya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

Domain ID domain_id	d1gyyb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.80 — Tautomerase/MIF
Superfamily Superfamily superfamily	d.80.1 — Tautomerase/MIF
Family Family family	d.80.1.1 — 4-oxalocrotonate tautomerase-like

CATH v4.4 (2 domains)

Domain ID domain_id	1gyyA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

Domain ID domain_id	1gyyB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	429 — Macrophage Migration Inhibitory Factor
Homologous superfamily homologous superfamily	10 — Macrophage Migration Inhibitory Factor

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Unit-cell length a length_a	44.700 Å
Unit-cell length b length_b	46.700 Å
Unit-cell length c length_c	76.200 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	1.350 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1510
R_free r_free	0.1730

The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity

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

HYPOTHETICAL PROTEIN YDCE

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

1gyy__assembly_1__model_1

1gyy__assembly_1__model_1 | I(q)

1gyy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity

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

HYPOTHETICAL PROTEIN YDCE

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

1gyy__assembly_1__model_1

1gyy__assembly_1__model_1 | I(q)

1gyy__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)