3r8f

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

Method: X-RAY DIFFRACTION

▼

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

Chromosomal replication initiator protein dnaA

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 4 DNA 1	5'-D(PAPAPAPAPAPAPAPAPAPAPAPA)-3' × 1 MAGNESIUM ION × 4 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 4 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAA_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–324； UniProt 76–399 Author chain B； PDBConstruct 1–324； UniProt 76–399 Author chain C； PDBConstruct 1–324； UniProt 76–399 Author chain D； PDBConstruct 1–324； UniProt 76–399

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3r8f
Deposition date deposition_date	2011-03-23
Structure title title	Replication initiator DnaA bound to AMPPCP and single-stranded DNA
Keywords keywords	AAA+ ATPase, Replication Initiator, DNA Binding, REPLICATION ACTIVATOR-DNA complex; REPLICATION ACTIVATOR/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3r8f__assembly_1__model_1

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

Download this curve (.dat)

3r8f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r8f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.70 Å
Rg (electron density)	40.13 Å
Total Rg	40.37 Å
Atom count	10852
Residues	1288
Excluded volume	194060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r8f__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Chromosomal replication initiator protein dnaA
Molecular weight formula_weight	37862.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10874

KDFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(PAPAPAPAPAPAPAPAPAPAPAPA)-3'
Molecular weight formula_weight	3713.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

AAAAAAAAAAAA

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	22

▼

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3r8fA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3r8fA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3r8fA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1750 — Chromosomal Replication Initiator Protein Dnaa; Chain: A;
Homologous superfamily homologous superfamily	10 — DnaA protein, C-terminal DNA-binding domain

Domain ID domain_id	3r8fB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3r8fB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3r8fB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1750 — Chromosomal Replication Initiator Protein Dnaa; Chain: A;
Homologous superfamily homologous superfamily	10 — DnaA protein, C-terminal DNA-binding domain

Domain ID domain_id	3r8fC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3r8fC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3r8fC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1750 — Chromosomal Replication Initiator Protein Dnaa; Chain: A;
Homologous superfamily homologous superfamily	10 — DnaA protein, C-terminal DNA-binding domain

Domain ID domain_id	3r8fD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3r8fD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	3r8fD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1750 — Chromosomal Replication Initiator Protein Dnaa; Chain: A;
Homologous superfamily homologous superfamily	10 — DnaA protein, C-terminal DNA-binding domain

▶

Unit-cell length a length_a	99.797 Å
Unit-cell length b length_b	114.219 Å
Unit-cell length c length_c	201.266 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	16

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

Resolution resolution	3.366 Å
Low-resolution limit resolution_low	43.487 Å
R factor r_factor	0.2499
R_work r_work	0.2490
R_free r_free	0.2682

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

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

Chromosomal replication initiator protein dnaA

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

3r8f__assembly_1__model_1

3r8f__assembly_1__model_1 | I(q)

3r8f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Replication initiator DnaA bound to AMPPCP and single-stranded DNA

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

Chromosomal replication initiator protein dnaA

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

3r8f__assembly_1__model_1

3r8f__assembly_1__model_1 | I(q)

3r8f__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)