SAXSdb — 1wvg

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

CDP-glucose 4,6-dehydratase

Salmonella enterica subsp. enterica serovar Typhi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ADENOSINE-5-DIPHOSPHORIBOSE × 4 CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RFBG_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–359； UniProt 1–359 Author chain B； PDBConstruct 1–359； UniProt 1–359

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	1wvg
Deposition date deposition_date	2004-12-15
Structure title title	Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi
Keywords keywords	short-chain dehydrogenase/reductase, Rossmann fold, 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.

1wvg__assembly_1__model_1

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

Download this curve (.dat)

1wvg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wvg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.67 Å
Rg (electron density)	35.10 Å
Total Rg	35.67 Å
Atom count	11510
Residues	1404
Excluded volume	203540 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wvg__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	CDP-glucose 4,6-dehydratase
Molecular weight formula_weight	41030.5 kDa
EC 编号 ec_number	4.2.1.45
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	6098

SIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLFEIVRLNDLMESHIGDIRDFEKLRSSIAEFKPEIVFHMAAQPLVRLSYEQPIKTYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEPMGGYDPYSNSKGCAELVASAFRNSFFNPANYEQHGVGLASVRAGNVIGGGDWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLYTEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGDDASWLLDGENHPHEAHYLKLDCSKANMQLGWHPRWGLTETLSRIVKWHKAWIRGEDMLICSKREISDYMSATTR

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Typhi
NCBI taxonomy ID ncbi_taxonomy_id	220341
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5-DIPHOSPHORIBOSE
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
Molecular weight formula_weight	535.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wvga1
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

Domain ID domain_id	d1wvgb_
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 (4 domains)

Domain ID domain_id	1wvgA01
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	1wvgA02
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

Domain ID domain_id	1wvgB01
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	1wvgB02
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	93.900 Å
Unit-cell length b length_b	93.900 Å
Unit-cell length c length_c	152.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2030
R_work r_work	0.2010
R_free r_free	0.2700

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi

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

CDP-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

1wvg__assembly_1__model_1

1wvg__assembly_1__model_1 | I(q)

1wvg__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi

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

CDP-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

1wvg__assembly_1__model_1

1wvg__assembly_1__model_1 | I(q)

1wvg__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)