SAXSdb — 3koq

▼

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

NITROREDUCTASE FAMILY PROTEIN

Clostridium difficile

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 GLYCEROL × 7 CHLORIDE ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN MONONUCLEOTIDE × 2 GLYCEROL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q180K0_CLOD6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–191； UniProt 1–172 Author chain B； PDBConstruct 20–191； UniProt 1–172 Author chain C； PDBConstruct 20–191； UniProt 1–172 Author chain D； PDBConstruct 20–191； UniProt 1–172

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3koq
Deposition date deposition_date	2009-11-13
Structure title title	Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.58 A resolution
Keywords keywords	Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3koq__assembly_1__model_1

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

Download this curve (.dat)

3koq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3koq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.34 Å
Rg (electron density)	19.36 Å
Total Rg	20.17 Å
Atom count	2871
Residues	337
Excluded volume	51524 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3koq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3koq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NITROREDUCTASE FAMILY PROTEIN
Molecular weight formula_weight	22310.7 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	6969

MGSDKIHHHHHHENLYFQGMNFVELAKKRYSCRNYQDRKVEKEKLEKVLDVARIAPTGGNRQPQRLIVIQEKEGINKLSKAANIYDAPLAILVCGDKDKVWTRPFDGKQLTDIDTSIVTDHMMLQATELGLASVWVCYFNPDIIREEFSLPDNLEPINILLMGYESKIPESPERHEKTRVPLSEIVSYETL

Source Source

Source organism organism	Clostridium difficile
NCBI taxonomy ID ncbi_taxonomy_id	272563
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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	875

▼

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3koqa1
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	d3koqa2
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	d3koqb_
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	d3koqc_
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	d3koqd_
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	3koqA00
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	3koqB00
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	3koqC00
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	3koqD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	109 — NADH Oxidase
Homologous superfamily homologous superfamily	10 — NADH Oxidase

▶

Unit-cell length a length_a	58.369 Å
Unit-cell length b length_b	87.924 Å
Unit-cell length c length_c	87.501 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	29.374 Å
R factor r_factor	0.1800
R_work r_work	0.1780
R_free r_free	0.2180

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.58 A resolution

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

NITROREDUCTASE FAMILY 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

3koq__assembly_1__model_1

3koq__assembly_1__model_1 | I(q)

3koq__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a nitroreductase family protein (cd3355) from clostridium difficile 630 at 1.58 A resolution

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

NITROREDUCTASE FAMILY 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

3koq__assembly_1__model_1

3koq__assembly_1__model_1 | I(q)

3koq__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)