SAXSdb — 1r66

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

TDP-glucose-4,6-dehydratase

Streptomyces venezuelae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 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	Q9ZGH3_9ACTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–337； UniProt 1–337

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	1r66
Deposition date deposition_date	2003-10-14
Structure title title	Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound
Keywords keywords	Dehydratase, Rossmann Fold, Short-Chain Dehydrogenase/Reductase, LYASE; LYASE
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.

1r66__assembly_1__model_1

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

Download this curve (.dat)

1r66__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r66__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.95 Å
Rg (electron density)	26.37 Å
Total Rg	27.02 Å
Atom count	5089
Residues	644
Excluded volume	88958 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r66__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 (5)

Entity 1 Entity 1 polymer

Description description	TDP-glucose-4,6-dehydratase
Molecular weight formula_weight	36499.9 kDa
EC 编号 ec_number	4.2.1.46
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	2835

MRLLVTGGAGFIGSHFVRQLLAGAYPDVPADEVIVLDSLTYAGNRANLAPVDADPRLRFVHGDIRDAGLLARELRGVDAIVHFAAESHVDRSIAGASVFTETNVQGTQTLLQCAVDAGVGRVVHVSTDEVYGSIDSGSWTESSPLEPNSPYAASKAGSDLVARAYHRTYGLDVRITRCCNNYGPYQHPEKLIPLFVTNLLDGGTLPLYGDGANVREWVHTDDHCRGIALVLAGGRAGEIYHIGGGLELTNRELTGILLDSLGADWSSVRKVADRKGHDLRYSLDGGKIERELGYRPQVSFADGLARTVRWYRENRGWWEPLKATAPQLPATAVEVSA

Source Source

Source organism organism	Streptomyces venezuelae
NCBI taxonomy ID ncbi_taxonomy_id	54571
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	273

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1r66a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (2 domains)

Domain ID domain_id	1r66A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	1r66A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	25 — UDP-galactose 4-epimerase; domain 1
Homologous superfamily homologous superfamily	10 — UDP-galactose 4-epimerase, domain 1

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Unit-cell length a length_a	75.501 Å
Unit-cell length b length_b	99.799 Å
Unit-cell length c length_c	42.187 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.440 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.1760
R_free r_free	0.2310

Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound

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

TDP-glucose-4,6-dehydratase

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

1r66__assembly_1__model_1

1r66__assembly_1__model_1 | I(q)

1r66__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of DesIV (dTDP-glucose 4,6-dehydratase) from Streptomyces venezuelae with NAD and TYD bound

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

TDP-glucose-4,6-dehydratase

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

1r66__assembly_1__model_1

1r66__assembly_1__model_1 | I(q)

1r66__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)