SAXSdb — 1epz

▼

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

DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE

Methanothermobacter thermautotrophicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THYMIDINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O27818_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 1–185

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1epz
Deposition date deposition_date	2000-03-30
Structure title title	CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.
Keywords keywords	racemase, dTDP-4-dehydrorhamnose epimerase, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1epz__assembly_1__model_1

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

Download this curve (.dat)

1epz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1epz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.46 Å
Rg (electron density)	21.64 Å
Total Rg	22.43 Å
Atom count	3086
Residues	366
Excluded volume	54290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1epz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
Molecular weight formula_weight	21702.3 kDa
EC 编号 ec_number	5.1.3.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1662

MAEFRFIKTSLDGAIIIEPEVYTDERGYFMETFNEAIFQENGLEVRFVQDNESMSVRGVLRGLHFQREKPQGKLVRVIRGEIFDVAVDLRKNSDTYGEWTGVRLSDENRREFFIPEGFAHGFLALSDECIVNYKCTELYHPEYDSGIPWDDPDIGIDWPLEMVDDLIISEKDRNWKPLRENPVYL

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	145262
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	THYMIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	402.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	119

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1epza_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.1 — dTDP-sugar isomerase

CATH v4.4 (1 domains)

Domain ID domain_id	1epzA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

▶

Unit-cell length a length_a	68.156 Å
Unit-cell length b length_b	53.486 Å
Unit-cell length c length_c	51.462 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2250

CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.

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

DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE

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

1epz__assembly_1__model_1

1epz__assembly_1__model_1 | I(q)

1epz__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF DTDP-6-DEOXY-D-XYLO-4-HEXULOASE 3,5-EPIMERASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM WITH BOUND LIGAND.

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

DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE

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

1epz__assembly_1__model_1

1epz__assembly_1__model_1 | I(q)

1epz__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)