SAXSdb — 6fk4

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

Exodeoxyribonuclease III

Neisseria meningitidis serogroup B (strain MC58)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(PGPCPTPAPGPCPGPAPAPGPCPTPAPGP*A)-3') ; × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K100_NEIMB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–258； UniProt 1–256

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	6fk4
Deposition date deposition_date	2018-01-23
Structure title title	Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate
Keywords keywords	;3' phosphatase, base excision DNA repair., DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

6fk4__assembly_1__model_1

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

Download this curve (.dat)

6fk4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fk4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.69 Å
Rg (electron density)	18.28 Å
Total Rg	19.30 Å
Atom count	2386
Residues	273
Excluded volume	41320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fk4__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 (4)

Entity 1 Entity 1 polymer

Description description	Exodeoxyribonuclease III
Molecular weight formula_weight	29318.4 kDa
EC 编号 ec_number	3.1.11.2
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	2451

GAMKITTWNVNSLNVRLPQVQNLLADNPPDILVLQELKLDQDKFPAAALQMMGWHCVWSGQKTYNGVAIVSRSVPQDVHFGLPALPDDPQRRVIAATVSGVRVINVYCVNGEALDSPKFKYKEQWFAALTEFVRDEMTRHGKLVLLGDFNIAPADADCYDPEKWHEKIHCSSVERQWFQNLLDLGLTDSLRQVHPEGAFYTWFDYRGAMFQRKLGLRIDHILVSPAMAAALKDVRVDLETRALERPSDHAPVTAEFDW

Source Source

Source organism organism	Neisseria meningitidis serogroup B (strain MC58)
NCBI taxonomy ID ncbi_taxonomy_id	122586
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PGPCPTPAPGPCPGPAPAPGPCPTPAPGP*A)-3') ;
Molecular weight formula_weight	5589.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

ATGGCTAGCGAAGCTAGA

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6fk4A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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Unit-cell length a length_a	59.156 Å
Unit-cell length b length_b	59.156 Å
Unit-cell length c length_c	292.091 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.297 Å
Low-resolution limit resolution_low	41.566 Å
R factor r_factor	0.2001
R_work r_work	0.1985
R_free r_free	0.2300

Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate

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

Exodeoxyribonuclease III

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

6fk4__assembly_1__model_1

6fk4__assembly_1__model_1 | I(q)

6fk4__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Structure of 3' phosphatase NExo (WT) from Neisseria bound to DNA substrate

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

Exodeoxyribonuclease III

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

6fk4__assembly_1__model_1

6fk4__assembly_1__model_1 | I(q)

6fk4__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)