SAXSdb — 3amf

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

FMN-binding protein

Desulfovibrio vulgaris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FMNB_DESVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 1–122 Author chain B； PDBConstruct 1–122； UniProt 1–122

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	3amf
Deposition date deposition_date	2010-08-19
Structure title title	E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Keywords keywords	ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

3amf__assembly_1__model_1

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

Download this curve (.dat)

3amf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3amf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.55 Å
Rg (electron density)	17.33 Å
Total Rg	18.28 Å
Atom count	1920
Residues	244
Excluded volume	34124 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3amf__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 (4)

Entity 1 Entity 1 polymer

Description description	FMN-binding protein
Molecular weight formula_weight	13181.1 kDa
Mutation mutation	E13R
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	2196

MLPGTFFEVLKNRGVVAIATQGEDGPHLVNTWNSYLKVLDGNRIVVPVGGMHKTEANVARDERVLMTLGSRKVAGRNGPGTGFLIRGSAAFRTDGPEFEAIARFKWARAALVITVVSAEQTL

Source Source

Source organism organism	Desulfovibrio vulgaris
NCBI taxonomy ID ncbi_taxonomy_id	883
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3amfa_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

Domain ID domain_id	d3amfb_
Class class	b — All beta proteins
Fold Fold fold	b.45 — Split barrel-like
Superfamily Superfamily superfamily	b.45.1 — FMN-binding split barrel
Family Family family	b.45.1.1 — PNP-oxidase like

CATH v4.4 (2 domains)

Domain ID domain_id	3amfA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

Domain ID domain_id	3amfB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	110 — Pnp Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Electron Transport, Fmn-binding Protein; Chain A

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Unit-cell length a length_a	54.129 Å
Unit-cell length b length_b	60.443 Å
Unit-cell length c length_c	72.002 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1942
R_work r_work	0.1926
R_free r_free	0.2238

E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

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

FMN-binding protein

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

3amf__assembly_1__model_1

3amf__assembly_1__model_1 | I(q)

3amf__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

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

FMN-binding protein

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

3amf__assembly_1__model_1

3amf__assembly_1__model_1 | I(q)

3amf__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)