SAXSdb — 1zd7

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

DNA polymerase III alpha subunit

Synechocystis sp.

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DP3A_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 775–933 Author chain B； PDBConstruct 1–159； UniProt 775–933

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	1zd7
Deposition date deposition_date	2005-04-14
Structure title title	1.7 Angstrom Crystal Structure Of Post-Splicing Form of a dnaE Intein from Synechocystis Sp. Pcc 6803
Keywords keywords	DnaE, Intein, Splicing, TRANSFERASE; TRANSFERASE
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.

1zd7__assembly_1__model_1

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

Download this curve (.dat)

1zd7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zd7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.72 Å
Rg (electron density)	15.21 Å
Total Rg	16.33 Å
Atom count	1274
Residues	158
Excluded volume	22585 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zd7__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zd7__assembly_2__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	DNA polymerase III alpha subunit
Molecular weight formula_weight	17919.1 kDa
EC 编号 ec_number	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	2778

CLSFGTEILTVEYGPLPIGKIVSEEINCSVYSVDPEGRVYTQAIAQWHDRGEQEVLEYELEDGSVIRATSDHRFLTTDYQLLAIEEIFARQLDLLTLENIKQTEEALDNHRLPFPLLDAGTIKMVKVIGRRSLGVQRIFDIGLPQDHNFLLANGAIAAN

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	240

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zd7a_
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.86.1.0 — automated matches

Domain ID domain_id	d1zd7b_
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.86.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	1zd7A00
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

Domain ID domain_id	1zd7B00
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	50.247 Å
Unit-cell length b length_b	67.035 Å
Unit-cell length c length_c	90.336 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	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1790
R_work r_work	0.1766
R_free r_free	0.2018

1.7 Angstrom Crystal Structure Of Post-Splicing Form of a dnaE Intein from Synechocystis Sp. Pcc 6803

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

DNA polymerase III alpha subunit

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

1zd7__assembly_1__model_1

1zd7__assembly_1__model_1 | I(q)

1zd7__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 (1)

1.7 Angstrom Crystal Structure Of Post-Splicing Form of a dnaE Intein from Synechocystis Sp. Pcc 6803

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

DNA polymerase III alpha subunit

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

1zd7__assembly_1__model_1

1zd7__assembly_1__model_1 | I(q)

1zd7__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 (1)