1eqn

E.COLI PRIMASE CATALYTIC CORE

Method: X-RAY DIFFRACTION

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

DNA PRIMASE

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	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIM_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 109–429 Author chain B； PDBConstruct 1–321； UniProt 109–429 Author chain C； PDBConstruct 1–321； UniProt 109–429 Author chain D； PDBConstruct 1–321； UniProt 109–429 Author chain E； PDBConstruct 1–321； UniProt 109–429

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	1eqn
Deposition date deposition_date	2000-04-05
Structure title title	E.COLI PRIMASE CATALYTIC CORE
Keywords keywords	Toprim domain, Rossmann fold, 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.

1eqn__assembly_1__model_1

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

Download this curve (.dat)

1eqn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1eqn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.46 Å
Rg (electron density)	22.82 Å
Total Rg	23.44 Å
Atom count	2462
Residues	306
Excluded volume	43655 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1eqn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1eqn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1eqn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1eqn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1eqn__assembly_5__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 (1)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1eqna_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d1eqnb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d1eqnc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d1eqnd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

Domain ID domain_id	d1eqne_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.13 — DNA primase core
Superfamily Superfamily superfamily	e.13.1 — DNA primase core
Family Family family	e.13.1.1 — DNA primase DnaG catalytic core

CATH v4.4 (15 domains)

Domain ID domain_id	1eqnA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	1eqnA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1eqnA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

Domain ID domain_id	1eqnB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	1eqnB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1eqnB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

Domain ID domain_id	1eqnC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	1eqnC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1eqnC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

Domain ID domain_id	1eqnD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	1eqnD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1eqnD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

Domain ID domain_id	1eqnE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	980 — DNA primase DNAg catalytic core, N-terminal domain
Homologous superfamily homologous superfamily	10 — DNA primase, catalytic core, N-terminal domain

Domain ID domain_id	1eqnE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1360 — Dna Topoisomerase Vi A Subunit; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1eqnE03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	50 — Pheromone ER-1
Homologous superfamily homologous superfamily	20 — DnaG, RNA polymerase domain, helical bundle

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Unit-cell length a length_a	62.674 Å
Unit-cell length b length_b	107.626 Å
Unit-cell length c length_c	263.069 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	20

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	0.2259
R_work r_work	0.2197
R_free r_free	0.2760

Description description	DNA PRIMASE
Molecular weight formula_weight	36620.9 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	5

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	12156

E.COLI PRIMASE CATALYTIC CORE

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

DNA PRIMASE

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

1eqn__assembly_1__model_1

1eqn__assembly_1__model_1 | I(q)

1eqn__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

CATH v4.4 (15 domains)

7. Citations (1)

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

E.COLI PRIMASE CATALYTIC CORE

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

DNA PRIMASE

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

1eqn__assembly_1__model_1

1eqn__assembly_1__model_1 | I(q)

1eqn__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (5 domains)

CATH v4.4 (15 domains)

7. Citations (1)