SAXSdb — 7dlv

▼

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

Orf20

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	shrimp dUTPase × 3 SULFATE ION × 4 CALCIUM ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	shrimp dUTPase × 3 SULFATE ION × 5 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9F0J8_STAAU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 3–157； UniProt 1–155 Author chain E； PDBConstruct 3–157； UniProt 1–155 Author chain F； PDBConstruct 3–157； UniProt 1–155 Author chain J； PDBConstruct 3–157； UniProt 1–155 Author chain K； PDBConstruct 3–157； UniProt 1–155 Author chain L； PDBConstruct 3–157； UniProt 1–155

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	7dlv
Deposition date deposition_date	2020-11-30
Structure title title	shrimp dUTPase in complex with Stl
Keywords keywords	dUTPase, Stl, dUTP, shrimp, Penaeus vannamei, Staphylococcus aureus, HYDROLASE; HYDROLASE
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.

7dlv__assembly_1__model_1

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

Download this curve (.dat)

7dlv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dlv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.83 Å
Rg (electron density)	29.88 Å
Total Rg	30.60 Å
Atom count	6719
Residues	832
Excluded volume	120050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dlv__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7dlv__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	shrimp dUTPase
Molecular weight formula_weight	16304.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,G,H,I
Atom count atom_count	13439

SNAPGELKSVLRFKKLTEHAFTPSKGSKFAAGFDLCSAYDLVIPAVGKALVKTDIQVELPEGCYGRIAPRSGLSWKHHIDVGAGVIDRDYRGNVGVVLFNHAKTDYEVKKGDRVAQLICEKIIYPEIQEVEELMETERGEGGFGSTGNQ

Source Source

Source organism organism	Penaeus vannamei
NCBI taxonomy ID ncbi_taxonomy_id	6689
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Orf20
Molecular weight formula_weight	18127.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,J,K,L

GAMEGAGQMAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIPSYILHRISDEFKEKGYSPTLNDFGKFDKMYSYVNKAYYNDGDIYYSSYDLYDETIKLLELLKESKINVNDIDYDYVLKLYKQILSTD

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

▶

Unit-cell length a length_a	74.702 Å
Unit-cell length b length_b	135.884 Å
Unit-cell length c length_c	135.627 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.525 Å
Low-resolution limit resolution_low	94.126 Å
R factor r_factor	0.1773
R_work r_work	0.1716
R_free r_free	0.2009

shrimp dUTPase in complex with Stl

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

Orf20

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

7dlv__assembly_1__model_1

7dlv__assembly_1__model_1 | I(q)

7dlv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

shrimp dUTPase in complex with Stl

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

Orf20

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

7dlv__assembly_1__model_1

7dlv__assembly_1__model_1 | I(q)

7dlv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)