SAXSdb — 4e3y

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

Nuclease

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 1,2-ETHANEDIOL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 1,2-ETHANEDIOL × 1 SULFATE ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUCA_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–245； UniProt 22–266 Author chain B； PDBConstruct 1–245； UniProt 22–266

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	4e3y
Deposition date deposition_date	2012-03-11
Structure title title	X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution
Keywords keywords	Rossmann Fold, Hydrolase, Nucleic Acid, Extracellular; 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.

4e3y__assembly_1__model_1

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

Download this curve (.dat)

4e3y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4e3y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.81 Å
Rg (electron density)	16.64 Å
Total Rg	17.73 Å
Atom count	3648
Residues	240
Excluded volume	32774 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4e3y__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4e3y__assembly_2__model_1`	monomeric （1）	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	Nuclease
Molecular weight formula_weight	26738.9 kDa
EC 编号 ec_number	3.1.30.2
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8507

DTLESIDNCAVGCPTGGSSNVSIVRHAYTLNNNSTTKFANWVAYHITKDTPASGKTRNWKTDPALNPADTLAPADYTGANAALKVDRGHQAPLASLAGVSDWESLNYLSNITPQKSDLNQGAWARLEDQERKLIDRADISSVYTVTGPLYERDMGKLPGTQKAHTIPSAYWKVIFINNSPAVNHYAAFLFDQNTPKGADFCQFRVTVDEIEKRTGLIIWAGLPDDVQASLKSKPGVLPELMGCKN

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	685

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4e3ya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.2 — DNA/RNA non-specific endonuclease

Domain ID domain_id	d4e3yb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.2 — DNA/RNA non-specific endonuclease

CATH v4.4 (2 domains)

Domain ID domain_id	4e3yA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	570 — Extracellular Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Extracellular Endonuclease, subunit A

Domain ID domain_id	4e3yB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	570 — Extracellular Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Extracellular Endonuclease, subunit A

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Unit-cell length a length_a	106.265 Å
Unit-cell length b length_b	73.418 Å
Unit-cell length c length_c	67.924 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	0.950 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1309
R_work r_work	0.1302
R_free r_free	0.1453

X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution

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

Nuclease

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

4e3y__assembly_1__model_1

4e3y__assembly_1__model_1 | I(q)

4e3y__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

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

X-ray structure of the Serratia marcescens endonuclease at 0.95 A resolution

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

Nuclease

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

4e3y__assembly_1__model_1

4e3y__assembly_1__model_1 | I(q)

4e3y__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

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)