SAXSdb — 2ygk

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

NURA

SULFOLOBUS SOLFATARICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97WH1_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–339； UniProt 1–339 Author chain B； PDBConstruct 1–339； UniProt 1–339

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	2ygk
Deposition date deposition_date	2011-04-18
Structure title title	Crystal structure of the NurA nuclease from Sulfolobus solfataricus
Keywords keywords	HYDROLASE, DNA REPAIR, REPLICATION; 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.

2ygk__assembly_1__model_1

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

Download this curve (.dat)

2ygk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ygk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.60 Å
Rg (electron density)	27.69 Å
Total Rg	28.38 Å
Atom count	5168
Residues	618
Excluded volume	93694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ygk__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 (3)

Entity 1 Entity 1 polymer

Description description	NURA
Molecular weight formula_weight	39649.2 kDa
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	5250

MIRKIYDKLVESHNEIKNQIYNIANYLKQEIQDKVNEYWNEYVINHEQSETCKFVAIDGGSFGRPMRIGIVYAVGAESVIGDNKGVKTLSEDGQIGIFKPGNDAQERISLLMEALELSLALRDGSKGDYILMDGSLSKKIGNKVDIQQFSDEELKLIRNVDLNGIISIKDERKMRDLLMLLNQFLVSKIIEEYDGNVLWISKVSRGRDLFGTDYPDITVLELFTEKRGFSKLIIKNIDIEKISEIPEIEVLRKMEYTTFYTRLDNGKRVIRVDIVGRVDEKIVKEIMDRLSGVSIKGYPFPLLKAHMDVRFSAMDREKIIKLVGSKLHKDIEWWPSQFY

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	2287
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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Unit-cell length a length_a	67.740 Å
Unit-cell length b length_b	80.280 Å
Unit-cell length c length_c	67.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.17 °
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	2.500 Å
Low-resolution limit resolution_low	35.940 Å
R factor r_factor	0.2338
R_work r_work	0.2318
R_free r_free	0.2709

Crystal structure of the NurA nuclease from Sulfolobus solfataricus

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

NURA

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

2ygk__assembly_1__model_1

2ygk__assembly_1__model_1 | I(q)

2ygk__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 water

7. Citations (1)

Crystal structure of the NurA nuclease from Sulfolobus solfataricus

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

NURA

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

2ygk__assembly_1__model_1

2ygk__assembly_1__model_1 | I(q)

2ygk__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 water

7. Citations (1)