SAXSdb — 3hej

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

Thermonuclease

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THYMIDINE-3',5'-DIPHOSPHATE × 2 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	THYMIDINE-3',5'-DIPHOSPHATE × 2 GLYCEROL × 1 (4R)-2-METHYLPENTANE-2,4-DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUC_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–143； UniProt 83–231 Author chain B； PDBConstruct 1–143； UniProt 83–231 Author chain C； PDBConstruct 1–143； UniProt 83–231 Author chain D； PDBConstruct 1–143； UniProt 83–231

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	3hej
Deposition date deposition_date	2009-05-08
Structure title title	Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature
Keywords keywords	;Staphylococcal nuclease, hyperstable variant, hydrolase, pdtp, domain swapping, arginine, Calcium, Endonuclease, Membrane, Metal-binding, Nuclease, Secreted, Zymogen ;; 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.

3hej__assembly_1__model_1

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

Download this curve (.dat)

3hej__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hej__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.82 Å
Rg (electron density)	23.27 Å
Total Rg	24.18 Å
Atom count	2224
Residues	270
Excluded volume	39940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hej__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hej__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 (6)

Entity 1 Entity 1 polymer

Description description	Thermonuclease
Molecular weight formula_weight	16199.6 kDa
EC 编号 ec_number	3.1.31.1
Mutation mutation	G50F, V51N, T62R, P117G, H124L, S128A, Del44-49
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,B,C
Atom count atom_count	5045

ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFRKKMVENAKKIEVEFDKGQRTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	THYMIDINE-3',5'-DIPHOSPHATE
Molecular weight formula_weight	402.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3heja_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.1 — Staphylococcal nuclease
Family Family family	b.40.1.1 — Staphylococcal nuclease

Domain ID domain_id	d3hejb_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.1 — Staphylococcal nuclease
Family Family family	b.40.1.1 — Staphylococcal nuclease

Domain ID domain_id	d3hejc_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.1 — Staphylococcal nuclease
Family Family family	b.40.1.1 — Staphylococcal nuclease

Domain ID domain_id	d3hejd_
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.1 — Staphylococcal nuclease
Family Family family	b.40.1.1 — Staphylococcal nuclease

CATH v4.4 (4 domains)

Domain ID domain_id	3hejA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3hejB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3hejC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3hejD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	90 —

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Unit-cell length a length_a	67.598 Å
Unit-cell length b length_b	74.420 Å
Unit-cell length c length_c	67.975 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.22 °
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	1.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2440

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature

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

Thermonuclease

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

3hej__assembly_1__model_1

3hej__assembly_1__model_1 | I(q)

3hej__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Staphylococcal nuclease variant Delta+PHS T62R at cryogenic temperature

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

Thermonuclease

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

3hej__assembly_1__model_1

3hej__assembly_1__model_1 | I(q)

3hej__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)