SAXSdb — 1v13

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

COLICIN E9

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA9_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–134； UniProt 450–582 Author chain B； PDBConstruct 2–134； UniProt 450–582

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	1v13
Deposition date deposition_date	2004-04-06
Structure title title	CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)
Keywords keywords	HOMING ENDONUCLEASES, COLICINS, BETA-BETA-ALPHA METAL ANTIBIOTIC, BACTERIOCIN, HYDROLASE, ENDONUCLEASE MOTIF, H-N-H MOTIF; 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.

1v13__assembly_1__model_1

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

Download this curve (.dat)

1v13__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v13__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.38 Å
Rg (electron density)	18.63 Å
Total Rg	19.59 Å
Atom count	1916
Residues	246
Excluded volume	33657 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v13__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 (3)

Entity 1 Entity 1 polymer

Description description	COLICIN E9
Molecular weight formula_weight	15053.0 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2009

MESKRNKPGKATGKGKPVGDKWLDDAGKDSGAPIPDRIADKLRDKEFKSFDDFRKAVWEEVSKDPELSKNLNPSNKSSVSKGYSPFTPKNQQVGGRKVYELHADKPISQGGEVYDMDNIRVTTPKRHIDIHRGK

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1v13a_
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	d1v13b_
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	1v13A00
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	1v13B00
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

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Unit-cell length a length_a	52.693 Å
Unit-cell length b length_b	61.441 Å
Unit-cell length c length_c	91.107 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.640 Å
R factor r_factor	0.2340
R_work r_work	0.2300
R_free r_free	0.3070

CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)

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

COLICIN E9

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

1v13__assembly_1__model_1

1v13__assembly_1__model_1 | I(q)

1v13__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-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 (2)

CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS)

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

COLICIN E9

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

1v13__assembly_1__model_1

1v13__assembly_1__model_1 | I(q)

1v13__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-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 (2)