SAXSdb — 3cxo

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

Putative galactonate dehydratase

Salmonella typhimurium LT2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	3,6-dideoxy-L-arabino-hexonic acid × 1 MAGNESIUM ION × 2 (2R,4S)-2,4,7-trihydroxyheptanoic acid × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	3,6-dideoxy-L-arabino-hexonic acid × 4 MAGNESIUM ION × 8 (2R,4S)-2,4,7-trihydroxyheptanoic acid × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZNF9_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–407； UniProt 2–405 Author chain B； PDBConstruct 4–407； UniProt 2–405

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	3cxo
Deposition date deposition_date	2008-04-24
Structure title title	Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and 3-deoxy-L-rhamnonate
Keywords keywords	L-rhamnonate dehydratase, enolase superfamily, 3-DEOXY-L-RHAMNONATE, 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.

3cxo__assembly_1__model_1

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

Download this curve (.dat)

3cxo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cxo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.17 Å
Rg (electron density)	26.20 Å
Total Rg	27.06 Å
Atom count	6247
Residues	804
Excluded volume	110910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cxo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cxo__assembly_2__model_1`	octameric （8）	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	Putative galactonate dehydratase
Molecular weight formula_weight	45975.3 kDa
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	6683

MSLENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSHEGHHHHHH

Source Source

Source organism organism	Salmonella typhimurium LT2
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	3,6-dideoxy-L-arabino-hexonic acid
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(2R,4S)-2,4,7-trihydroxyheptanoic acid
Molecular weight formula_weight	178.2 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	436

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3cxoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3cxoA02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

Domain ID domain_id	3cxoB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

Domain ID domain_id	3cxoB02
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	120 — Enolase-like C-terminal domain

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Unit-cell length a length_a	272.833 Å
Unit-cell length b length_b	272.833 Å
Unit-cell length c length_c	272.833 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	192

Space group space_group	F 4 3 2
Space-group number int_tables_number	209
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	24.910 Å
R factor r_factor	0.2210
R_work r_work	0.2210
R_free r_free	0.2340

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and 3-deoxy-L-rhamnonate

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

Putative galactonate 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

3cxo__assembly_1__model_1

3cxo__assembly_1__model_1 | I(q)

3cxo__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and 3-deoxy-L-rhamnonate

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

Putative galactonate 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

3cxo__assembly_1__model_1

3cxo__assembly_1__model_1 | I(q)

3cxo__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)