SAXSdb — 3ejk

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

dTDP Sugar Isomerase

Desulfovibrio desulfuricans subsp. desulfuricans str. G20

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	UNKNOWN LIGAND × 2 CITRIC ACID × 4 TETRAETHYLENE GLYCOL × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q30V07_DESDG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–174； UniProt 1–173

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	3ejk
Deposition date deposition_date	2008-09-18
Structure title title	Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution
Keywords keywords	;YP_390184.1, dTDP Sugar Isomerase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3ejk__assembly_1__model_1

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

Download this curve (.dat)

3ejk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ejk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.00 Å
Rg (electron density)	20.12 Å
Total Rg	20.81 Å
Atom count	2516
Residues	310
Excluded volume	44855 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ejk__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 (6)

Entity 1 Entity 1 polymer

Description description	dTDP Sugar Isomerase
Molecular weight formula_weight	19319.3 kDa
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	1417

GMDIMLNTADISAAAILLPVEGAQLSELRQIPAEGGPVLHMLRLDSPQFSQFGEIYFSEVLPRRVKAWKRHSLMTQLFAVPVGCIHVVLYDGREKSPTSGRLAQVTLGRPDNYRLLRIPPQVWYGFAATGDTPALVANCTDIPHRQGESERAPQDAPFIPFSWAGADLSGTPVM

Source Source

Source organism organism	Desulfovibrio desulfuricans subsp. desulfuricans str. G20
NCBI taxonomy ID ncbi_taxonomy_id	207559
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3ejkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	81.790 Å
Unit-cell length b length_b	86.510 Å
Unit-cell length c length_c	51.340 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	29.722 Å
R factor r_factor	0.1710
R_work r_work	0.1690
R_free r_free	0.2170

Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution

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

dTDP Sugar Isomerase

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

3ejk__assembly_1__model_1

3ejk__assembly_1__model_1 | I(q)

3ejk__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of dTDP Sugar Isomerase (YP_390184.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.95 A resolution

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

dTDP Sugar Isomerase

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

3ejk__assembly_1__model_1

3ejk__assembly_1__model_1 | I(q)

3ejk__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)