SAXSdb — 3gag

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

Putative NADH dehydrogenase, NADPH nitroreductase

Streptococcus mutans

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 SULFATE ION × 1 GLYCEROL × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 SULFATE ION × 1 GLYCEROL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DVW4_STRMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–206； UniProt 1–205 Author chain B； PDBConstruct 2–206； UniProt 1–205 Author chain C； PDBConstruct 2–206； UniProt 1–205 Author chain D； PDBConstruct 2–206； UniProt 1–205

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	3gag
Deposition date deposition_date	2009-02-17
Structure title title	Crystal structure of a nitroreductase-like protein (smu.346) from streptococcus mutans at 1.70 A resolution
Keywords keywords	;Fmn-dependent nitroreductase-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, oxidoreductase ;; OXIDOREDUCTASE
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.

3gag__assembly_2__model_1

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

Download this curve (.dat)

3gag__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gag__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.45 Å
Rg (electron density)	20.42 Å
Total Rg	21.26 Å
Atom count	3319
Residues	393
Excluded volume	59326 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gag__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gag__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative NADH dehydrogenase, NADPH nitroreductase
Molecular weight formula_weight	23859.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7575

GMMNDYLNFLDGRVSVRRFDPDAVLPNDLIKDMLEHASYAPSGNNFQPWRVVVVKNKNKQEDLKKLAALQPQVATASAVFLLFGDENAYDLTWWQEFHVQKGIITKDEAAARAERIRQYFDLHPEDKETQGLRLDVGLFAMNLMQVVRVYGYDSVPMRGVDFDAIKTYLDMPNGWEPILMLPVGKALQAGNPHVRKSVAEFAEIIE

Source Source

Source organism organism	Streptococcus mutans
NCBI taxonomy ID ncbi_taxonomy_id	1309
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	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	644

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3gaga1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.0 — automated matches

Domain ID domain_id	d3gaga2
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

Domain ID domain_id	d3gagb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.0 — automated matches

Domain ID domain_id	d3gagc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.0 — automated matches

Domain ID domain_id	d3gagc2
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

Domain ID domain_id	d3gagd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.90 — FMN-dependent nitroreductase-like
Superfamily Superfamily superfamily	d.90.1 — FMN-dependent nitroreductase-like
Family Family family	d.90.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3gagA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

Domain ID domain_id	3gagB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

Domain ID domain_id	3gagC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

Domain ID domain_id	3gagD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

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Unit-cell length a length_a	49.112 Å
Unit-cell length b length_b	52.478 Å
Unit-cell length c length_c	93.105 Å
Unit-cell angle α angle_alpha	88.13 °
Unit-cell angle β angle_beta	80.35 °
Unit-cell angle γ angle_gamma	62.14 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	29.591 Å
R factor r_factor	0.1540
R_work r_work	0.1520
R_free r_free	0.1880

Crystal structure of a nitroreductase-like protein (smu.346) from streptococcus mutans at 1.70 A resolution

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

Putative NADH dehydrogenase, NADPH nitroreductase

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

3gag__assembly_2__model_1

3gag__assembly_2__model_1 | I(q)

3gag__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a nitroreductase-like protein (smu.346) from streptococcus mutans at 1.70 A resolution

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

Putative NADH dehydrogenase, NADPH nitroreductase

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

3gag__assembly_2__model_1

3gag__assembly_2__model_1 | I(q)

3gag__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 (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) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)