SAXSdb — 3fbd

▼

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

Colicin-E7

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3' × 2 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3' × 2 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 445–576 Author chain D； PDBConstruct 1–132； UniProt 445–576

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	3fbd
Deposition date deposition_date	2008-11-19
Structure title title	Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA
Keywords keywords	;Computational redesign, Protein engineering, Protein-nucleic acid interactions, DNase, DNA hydrolysis., Antibiotic, Antimicrobial, Bacteriocin, Endonuclease, Hydrolase, Metal-binding, Nuclease, Plasmid, Zinc, HYDROLASE-DNA COMPLEX ;; HYDROLASE/DNA
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.

3fbd__assembly_1__model_1

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

Download this curve (.dat)

3fbd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fbd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.98 Å
Rg (electron density)	19.02 Å
Total Rg	19.87 Å
Atom count	1799
Residues	168
Excluded volume	29487 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fbd__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fbd__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Colicin-E7
Molecular weight formula_weight	15162.2 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	D493Q
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	3663

SKRNKPGKATGKGKPVNNKWLNNAGKDLGSPVPDRIANKLRDKEFKSFQDFRKKFWEEVSKDPELSKQFSRNNNDRMKVGKAPKTRTQDVSGKRTSFELHHEKPISQNGGVYDMDNISVVTPKRHIDIHRGK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(DGPDGPDAPDAPDTPDTPDCPDGPDAPDTPDCPDGPDAPDAPDTPDTPDCPDC)-3'
Molecular weight formula_weight	5515.6 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B,C,E,F

GGAATTCGATCGAATTCC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3fbda_
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.4.1.1 — HNH-motif

Domain ID domain_id	d3fbdd_
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.4.1.1 — HNH-motif

CATH v4.4 (2 domains)

Domain ID domain_id	3fbdA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
Homologous superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

Domain ID domain_id	3fbdD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain
Homologous superfamily homologous superfamily	10 — Colicin/pyocin, DNase domain

▶

Unit-cell length a length_a	60.587 Å
Unit-cell length b length_b	49.423 Å
Unit-cell length c length_c	92.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.64 °
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	2.900 Å
Low-resolution limit resolution_low	27.200 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2640

Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA

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

Colicin-E7

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

3fbd__assembly_1__model_1

3fbd__assembly_1__model_1 | I(q)

3fbd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP duplex DNA

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

Colicin-E7

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

3fbd__assembly_1__model_1

3fbd__assembly_1__model_1 | I(q)

3fbd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)