SAXSdb — 3ef8

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

Putative Scyalone Dehydratase

Novosphingobium aromaticivorans DSM 12444

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	MAGNESIUM ION × 3 DI(HYDROXYETHYL)ETHER × 9 TRIETHYLENE GLYCOL × 12 TETRAETHYLENE GLYCOL × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	DI(HYDROXYETHYL)ETHER × 6 TETRAETHYLENE GLYCOL × 9 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2G8B5_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–150； UniProt 1–149 Author chain B； PDBConstruct 2–150； UniProt 1–149

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	3ef8
Deposition date deposition_date	2008-09-08
Structure title title	Crystal structure of Putative Scytalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution
Keywords keywords	;YP_496742.1, Putative Scytalone Dehydratase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function, 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.

3ef8__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ef8__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ef8__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.11 Å
Rg (electron density)	21.16 Å
Total Rg	21.91 Å
Atom count	3690
Residues	429
Excluded volume	65554 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ef8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ef8__assembly_2__model_1`	trimeric （3）	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	Putative Scyalone Dehydratase
Molecular weight formula_weight	17572.8 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	2797

GMTDTNLVEMRAIERMMFDYSYHLDMNHPEELAALFVEDCEVSYAPNFGATGRDAYKKTLEGIGTFFRGTSHHNSNICIDFVSETEANVRSVVLAIHRYTKERPDGILYGQYFDTVVKVDGQWKFKRRELRTTMTTDYHVRAANPIGRAE

Source Source

Source organism organism	Novosphingobium aromaticivorans DSM 12444
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	232

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ef8a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.28 — BaiE/LinA-like

Domain ID domain_id	d3ef8b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.28 — BaiE/LinA-like

CATH v4.4 (2 domains)

Domain ID domain_id	3ef8A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3ef8B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	59.851 Å
Unit-cell length b length_b	59.851 Å
Unit-cell length c length_c	237.504 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	29.921 Å
R factor r_factor	0.1640
R_work r_work	0.1630
R_free r_free	0.1880

Crystal structure of Putative Scytalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution

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

Putative Scyalone 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

3ef8__assembly_2__model_1

3ef8__assembly_2__model_1 | I(q)

3ef8__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Putative Scytalone Dehydratase (YP_496742.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.50 A resolution

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

Putative Scyalone 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

3ef8__assembly_2__model_1

3ef8__assembly_2__model_1 | I(q)

3ef8__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)