SAXSdb — 5ol5

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

DNA polymerase III subunit alpha,DNA polymerase III subunit alpha

Synechocystis sp. (strain PCC 6803 / Kazusa)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 TETRAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3A_SYNY3
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–34； UniProt 898–931 Author chain A； PDBConstruct 44–165； UniProt 776–897 Author chain B； PDBConstruct 1–34； UniProt 898–931 Author chain B； PDBConstruct 44–165； UniProt 776–897 Author chain C； PDBConstruct 1–34； UniProt 898–931 Author chain C； PDBConstruct 44–165； UniProt 776–897 Author chain D； PDBConstruct 1–34； UniProt 898–931 Author chain D； PDBConstruct 44–165； UniProt 776–897

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	5ol5
Deposition date deposition_date	2017-07-26
Structure title title	Crystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein
Keywords keywords	intein, extein, SICLOPPS, cyclic peptide, SPLICING; SPLICING
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.

5ol5__assembly_1__model_1

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

Download this curve (.dat)

5ol5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ol5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.34 Å
Rg (electron density)	13.99 Å
Total Rg	15.20 Å
Atom count	1113
Residues	139
Excluded volume	19804 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ol5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ol5__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ol5__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ol5__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 (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
Molecular weight formula_weight	19393.8 kDa
EC 编号 ec_number	2.7.7.7,2.7.7.7
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	4607

MVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAHACFAHPQALSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGEQEVLEYELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENIKQTEEALDNHRLPFPLLDAGTIKHHHHHH

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA polymerase III subunit alpha,DNA polymerase III subunit alpha
Molecular weight formula_weight	19377.8 kDa
EC 编号 ec_number	2.7.7.7,2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAHACFAHPQALSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGEQEVLEYELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENIKQTEEALDNHRLPFPLLDAGTIKHHHHHH

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 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 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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Unit-cell length a length_a	60.120 Å
Unit-cell length b length_b	92.129 Å
Unit-cell length c length_c	110.448 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.329 Å
Low-resolution limit resolution_low	55.224 Å
R factor r_factor	0.2331
R_work r_work	0.2309
R_free r_free	0.2759

Crystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein

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

DNA polymerase III subunit alpha,DNA polymerase III subunit alpha

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

5ol5__assembly_1__model_1

5ol5__assembly_1__model_1 | I(q)

5ol5__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of an inactivated Ssp SICLOPPS intein with CFAHPQ extein

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

DNA polymerase III subunit alpha,DNA polymerase III subunit alpha

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

5ol5__assembly_1__model_1

5ol5__assembly_1__model_1 | I(q)

5ol5__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)