SAXSdb — 3b39

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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–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ; × 1 water × 2	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ; × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRIM_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–322； UniProt 111–429 Author chain B； PDBConstruct 4–322； UniProt 111–429

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	3b39
Deposition date deposition_date	2007-10-19
Structure title title	Structure of the DnaG primase catalytic domain bound to ssDNA
Keywords keywords	;Protein-DNA complex, TOPRIM fold, DNA replication, DNA-directed RNA polymerase, Metal-binding, Nucleotidyltransferase, Primosome, Transcription, Transferase, Zinc-finger, transferase-DNA COMPLEX ;; transferase/DNA
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.

3b39__assembly_1__model_1

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

Download this curve (.dat)

3b39__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b39__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.86 Å
Rg (electron density)	23.00 Å
Total Rg	23.74 Å
Atom count	2619
Residues	323
Excluded volume	45869 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b39__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3b39__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(DCPDAPDAPDAPDGPDCPDCPDAPDAPDAPDAPDGPDGPDAP*DC)-3') ;
Molecular weight formula_weight	4605.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	5354

CAAAGCCAAAAGGAC

Entity 2 Entity 2 polymer

Description description	DNA primase
Molecular weight formula_weight	36289.0 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

SNAHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWCALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQLER

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3b39a1
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	d3b39a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3b39b1
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	d3b39b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	3b39A01
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	3b39A02
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	3b39A03
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	3b39B01
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	3b39B02
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	3b39B03
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	136.829 Å
Unit-cell length b length_b	136.829 Å
Unit-cell length c length_c	71.071 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 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2140
R_work r_work	0.2119
R_free r_free	0.2544

Structure of the DnaG primase catalytic domain bound to ssDNA

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

3b39__assembly_1__model_1

3b39__assembly_1__model_1 | I(q)

3b39__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of the DnaG primase catalytic domain bound to ssDNA

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

3b39__assembly_1__model_1

3b39__assembly_1__model_1 | I(q)

3b39__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)