SAXSdb — 3cng

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

NUDIX hydrolase

Nitrosomonas europaea ATCC 19718

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SODIUM ION × 2 CHLORIDE ION × 5 1,2-ETHANEDIOL × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 CHLORIDE ION × 2 1,2-ETHANEDIOL × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q82VD6_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–187； UniProt 1–185 Author chain B； PDBConstruct 3–187； UniProt 1–185 Author chain C； PDBConstruct 3–187； UniProt 1–185 Author chain D； PDBConstruct 3–187； UniProt 1–185

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	3cng
Deposition date deposition_date	2008-03-25
Structure title title	Crystal structure of NUDIX hydrolase from Nitrosomonas europaea
Keywords keywords	;structural genomics, APC7497, NUDIX hydrolase, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, HYDROLASE ;; HYDROLASE
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.

3cng__assembly_1__model_1

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

Download this curve (.dat)

3cng__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cng__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.11 Å
Rg (electron density)	22.13 Å
Total Rg	22.82 Å
Atom count	2904
Residues	345
Excluded volume	52279 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cng__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cng__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 (7)

Entity 1 Entity 1 polymer

Description description	NUDIX hydrolase
Molecular weight formula_weight	21846.5 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	6189

GHMKFCSQCGGEVILRIPEGDTLPRYICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYSLPHISQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFHLGIINKPQAGSNSNEGS

Source Source

Source organism organism	Nitrosomonas europaea ATCC 19718
NCBI taxonomy ID ncbi_taxonomy_id	228410
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

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	7

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	343

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3cngA01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3cngA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3cngB01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3cngB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3cngC01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3cngC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

Domain ID domain_id	3cngD01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3cngD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily	10 — Nucleoside Triphosphate Pyrophosphohydrolase

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Unit-cell length a length_a	174.781 Å
Unit-cell length b length_b	49.506 Å
Unit-cell length c length_c	110.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.28 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.200 Å
R factor r_factor	0.1830
R_work r_work	0.1810
R_free r_free	0.2330

Crystal structure of NUDIX hydrolase from Nitrosomonas europaea

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

NUDIX hydrolase

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

3cng__assembly_1__model_1

3cng__assembly_1__model_1 | I(q)

3cng__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of NUDIX hydrolase from Nitrosomonas europaea

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

NUDIX hydrolase

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

3cng__assembly_1__model_1

3cng__assembly_1__model_1 | I(q)

3cng__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)