SAXSdb — 1mi8

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

DnaB intein

Synechocystis sp.

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAB_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 379–478 Author chain A； PDBConstruct 118–158； UniProt 771–811

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	1mi8
Deposition date deposition_date	2002-08-22
Structure title title	2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803
Keywords keywords	all beta-strands, 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.

1mi8__assembly_1__model_1

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

Download this curve (.dat)

1mi8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1mi8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.88 Å
Rg (electron density)	22.27 Å
Total Rg	23.09 Å
Atom count	2214
Residues	282
Excluded volume	39855 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1mi8__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 (2)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1mi8a_
Class class	b — All beta proteins
Fold Fold fold	b.86 — Hedgehog/intein (Hint) domain
Superfamily Superfamily superfamily	b.86.1 — Hedgehog/intein (Hint) domain
Family Family family	b.86.1.2 — Intein (protein splicing domain)

CATH v4.4 (1 domains)

Domain ID domain_id	1mi8A00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	16 — Endonuclease - Pi-scei; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Hedgehog/Intein (Hint) domain

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Unit-cell length a length_a	58.170 Å
Unit-cell length b length_b	58.170 Å
Unit-cell length c length_c	70.280 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2260
R_work r_work	0.2100
R_free r_free	0.2630

Description description	DnaB intein
Molecular weight formula_weight	17600.2 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1157

2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803

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

DnaB intein

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

1mi8__assembly_1__model_1

1mi8__assembly_1__model_1 | I(q)

1mi8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Source organism organism	Synechocystis sp.
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

2.0 Angstrom crystal structure of a DnaB intein from Synechocystis sp. PCC 6803

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

DnaB intein

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

1mi8__assembly_1__model_1

1mi8__assembly_1__model_1 | I(q)

1mi8__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)