SAXSdb — 2r5r

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

UPF0343 protein NE1163

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 4	PHOSPHATE ION × 4 IMIDAZOLE × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1163_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–271； UniProt 1–268

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	2r5r
Deposition date deposition_date	2007-09-04
Structure title title	The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718
Keywords keywords	;APC86493, DUF198, Nitrosomonas europaea ATCC 19718, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2r5r__assembly_1__model_1

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

Download this curve (.dat)

2r5r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.85 Å
Rg (electron density)	28.44 Å
Total Rg	29.24 Å
Atom count	7952
Residues	964
Excluded volume	140700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5r__assembly_1__model_1`	tetrameric （4）	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 (3)

Entity 1 Entity 1 polymer

Description description	UPF0343 protein NE1163
Molecular weight formula_weight	31201.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1988

SNAMNKQIDLPIADVQGSLDTRHIAIDRVGIKAIRHPVVVADKGGGSQHTVAQFNMYVNLPHNFKGTHMSRFVEILNSHEREISVESFEEILRSMVSRLESDSGHIEMAFPYFINKSAPVSGVKSLLDYEVTFIGEIKHGNQYSFTMKVIVPVTSLCPCSKKISDYGAHNQRSHVTISVRTNSFIWIEDIIRIAEEQASCELYGLLKRPDEKYVTERAYNNPKFVEDIVRDVAEVLNHDDRIDAYIVESENFESIHNHSAYALIERDKRIR

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2r5rA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

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Unit-cell length a length_a	118.705 Å
Unit-cell length b length_b	118.705 Å
Unit-cell length c length_c	113.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.050 Å
Low-resolution limit resolution_low	38.870 Å
R factor r_factor	0.2401
R_work r_work	0.2391
R_free r_free	0.2605

The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718

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

UPF0343 protein NE1163

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

2r5r__assembly_1__model_1

2r5r__assembly_1__model_1 | I(q)

2r5r__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

The crystal structure of DUF198 from Nitrosomonas europaea ATCC 19718

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

UPF0343 protein NE1163

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

2r5r__assembly_1__model_1

2r5r__assembly_1__model_1 | I(q)

2r5r__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)