SAXSdb — 3bem

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

Putative NAD(P)H nitroreductase ydfN

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NICKEL (II) ION × 1 ACETATE ION × 1 FLAVIN MONONUCLEOTIDE × 2 S-1,2-PROPANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDFN_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–218； UniProt 1–206 Author chain B； PDBConstruct 13–218； UniProt 1–206

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	3bem
Deposition date deposition_date	2007-11-19
Structure title title	Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution
Keywords keywords	;2632848, putative nitroreductase ydfN, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Flavoprotein, FMN, NAD, NADP, 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.

3bem__assembly_1__model_1

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

Download this curve (.dat)

3bem__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bem__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.76 Å
Rg (electron density)	20.82 Å
Total Rg	21.44 Å
Atom count	3353
Residues	397
Excluded volume	59838 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bem__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 (6)

Entity 1 Entity 1 polymer

Description description	Putative NAD(P)H nitroreductase ydfN
Molecular weight formula_weight	25392.2 kDa
EC 编号 ec_number	1.-.-.-
Mutation mutation	K147A, E148A, K149A
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	3857

MGSDKIHHHHHHMAEFTHLVNERRSASNFLSGHPITKEDLNEMFELVALAPSAFNLQHTKYVTVLDQDVKEKLKQAANGQYKVVSSSAVLLVLGDKQAYQQAADIYEGLKVLGILNKQEYDHMVQDTVSFYENRGEQFKRDEAIRNASLSAMMFMLSAAAAGWDTCPMIGFDAEAVKRILNIDDQFEVVMMITIGKEKTESRRPRGYRKPVNEFVEYM

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	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	S-1,2-PROPANEDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3bema1
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	d3bema2
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	d3bemb1
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	d3bemb2
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	3bemA00
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	3bemB00
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	51.620 Å
Unit-cell length b length_b	69.200 Å
Unit-cell length c length_c	61.850 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	28.583 Å
R factor r_factor	0.1520
R_work r_work	0.1510
R_free r_free	0.1750

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution

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

Putative NAD(P)H nitroreductase ydfN

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

3bem__assembly_1__model_1

3bem__assembly_1__model_1 | I(q)

3bem__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 (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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of putative nitroreductase ydfN (2632848) from Bacillus subtilis at 1.65 A resolution

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

Putative NAD(P)H nitroreductase ydfN

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

3bem__assembly_1__model_1

3bem__assembly_1__model_1 | I(q)

3bem__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 (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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)