SAXSdb — 3fys

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

Protein degV

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PALMITIC ACID × 1 1,2-ETHANEDIOL × 1 BROMIDE ION × 7 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEGV_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 35–315； UniProt 1–281

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	3fys
Deposition date deposition_date	2009-01-23
Structure title title	Crystal Structure of DegV, a fatty acid binding protein from Bacillus subtilis
Keywords keywords	FATTY ACID-BINDING, EDD fold, FATTY ACID-BINDING PROTEIN; FATTY ACID-BINDING PROTEIN
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.

3fys__assembly_1__model_1

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

Download this curve (.dat)

3fys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fys__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.93 Å
Rg (electron density)	18.63 Å
Total Rg	19.68 Å
Atom count	2259
Residues	282
Excluded volume	40623 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fys__assembly_1__model_1`	monomeric （1）	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	Protein degV
Molecular weight formula_weight	35173.1 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	2391

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMNIAVVTDSTAYIPKEMREQHQIHMIPLQVVFREETYREEIELDWKSFYEEVKKHNELPTTSQPPIGELVALYEELGKSYDAVISIHLSSGISGTFSSAAAADSMVDNIDVYPFDSEISCLAQGFYALKAAELIKNGASSPEDIIKELEEMKKTVRAYFMVDDLAHLQRGGRLSSAQAFIGSLLKVKPILHFDNKVIVPFEKIRTRKKAISRIYELLDEDASKGLPMRAAVIHANREEEAAKIIEELSAKYPHVEFYNSYFGAVIGTHLGEGALGICWCFK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	132

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fysa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.0 — automated matches

Domain ID domain_id	d3fysa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3fysA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10170 —

Domain ID domain_id	3fysA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	42.100 Å
Unit-cell length b length_b	84.700 Å
Unit-cell length c length_c	42.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	11.953 Å
R factor r_factor	0.1523
R_work r_work	0.1485
R_free r_free	0.2246

Crystal Structure of DegV, a fatty acid binding protein from Bacillus subtilis

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

Protein degV

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

3fys__assembly_1__model_1

3fys__assembly_1__model_1 | I(q)

3fys__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of DegV, a fatty acid binding protein from Bacillus subtilis

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

Protein degV

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

3fys__assembly_1__model_1

3fys__assembly_1__model_1 | I(q)

3fys__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

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)