SAXSdb — 2a8k

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

Colicin E5

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CEA5_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–108； UniProt 74–180 Author chain B； PDBConstruct 2–108； UniProt 74–180 Author chain C； PDBConstruct 2–108； UniProt 74–180 Author chain D； PDBConstruct 2–108； UniProt 74–180

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	2a8k
Deposition date deposition_date	2005-07-08
Structure title title	Structural and Mutational Studies of the Catalytic Domain of Colicin E5a tRNA-Specific Ribonuclease
Keywords keywords	Ribonuclease, Toxin, HYDROLASE; 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.

2a8k__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2a8k__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2a8k__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	13.95 Å
Rg (electron density)	12.78 Å
Total Rg	14.05 Å
Atom count	739
Residues	94
Excluded volume	12938 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2a8k__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2a8k__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2a8k__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2a8k__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	Colicin E5
Molecular weight formula_weight	11996.3 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3302

MLAKNKGKIPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKNDQ

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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	346

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2a8ka1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.243 — Colicin D/E5 nuclease domain
Superfamily Superfamily superfamily	d.243.1 — Colicin D/E5 nuclease domain
Family Family family	d.243.1.2 — Colicin E5 nuclease domain

Domain ID domain_id	d2a8kb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.243 — Colicin D/E5 nuclease domain
Superfamily Superfamily superfamily	d.243.1 — Colicin D/E5 nuclease domain
Family Family family	d.243.1.2 — Colicin E5 nuclease domain

Domain ID domain_id	d2a8kc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.243 — Colicin D/E5 nuclease domain
Superfamily Superfamily superfamily	d.243.1 — Colicin D/E5 nuclease domain
Family Family family	d.243.1.2 — Colicin E5 nuclease domain

Domain ID domain_id	d2a8kd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.243 — Colicin D/E5 nuclease domain
Superfamily Superfamily superfamily	d.243.1 — Colicin D/E5 nuclease domain
Family Family family	d.243.1.2 — Colicin E5 nuclease domain

CATH v4.4 (4 domains)

Domain ID domain_id	2a8kA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	30 — Colicin E5 C-terminal ribonuclease domain (CRD)

Domain ID domain_id	2a8kB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	30 — Colicin E5 C-terminal ribonuclease domain (CRD)

Domain ID domain_id	2a8kC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	30 — Colicin E5 C-terminal ribonuclease domain (CRD)

Domain ID domain_id	2a8kD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2310 — YaeB-like fold
Homologous superfamily homologous superfamily	30 — Colicin E5 C-terminal ribonuclease domain (CRD)

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Unit-cell length a length_a	65.220 Å
Unit-cell length b length_b	65.220 Å
Unit-cell length c length_c	100.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2170
R_free r_free	0.2340

Structural and Mutational Studies of the Catalytic Domain of Colicin E5a tRNA-Specific Ribonuclease

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

Colicin E5

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

2a8k__assembly_4__model_1

2a8k__assembly_4__model_1 | I(q)

2a8k__assembly_4__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structural and Mutational Studies of the Catalytic Domain of Colicin E5a tRNA-Specific Ribonuclease

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

Colicin E5

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

2a8k__assembly_4__model_1

2a8k__assembly_4__model_1 | I(q)

2a8k__assembly_4__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)