2hcb

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

Method: X-RAY DIFFRACTION

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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 homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 4 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 4	Consistent with protein count

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 1–323； UniProt 77–399 Author chain B； PDBConstruct 1–323； UniProt 77–399 Author chain C； PDBConstruct 1–323； UniProt 77–399 Author chain D； PDBConstruct 1–323； UniProt 77–399

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2hcb
Deposition date deposition_date	2006-06-15
Structure title title	Structure of AMPPCP-bound DnaA from Aquifex aeolicus
Keywords keywords	AAA+ ATPase, Helix-turn-helix, REPLICATION; REPLICATION
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.

2hcb__assembly_1__model_1

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

Download this curve (.dat)

2hcb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hcb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.32 Å
Rg (electron density)	40.46 Å
Total Rg	40.71 Å
Atom count	10565
Residues	1272
Excluded volume	189910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hcb__assembly_1__model_1`	tetrameric （4）	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	Chromosomal replication initiator protein dnaA
Molecular weight formula_weight	37732.8 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	10565

DFLNPKYTLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIELDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTKNVREIEGKIKLIKLKGFEGLERKERKERDKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKKDRKFKHLVGFLEKQAFDKIC

Source Source

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

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 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

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2hcba1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.2 — Chromosomal replication initiation factor DnaA C-terminal domain IV

Domain ID domain_id	d2hcba2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d2hcbb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.2 — Chromosomal replication initiation factor DnaA C-terminal domain IV

Domain ID domain_id	d2hcbb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d2hcbc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.2 — Chromosomal replication initiation factor DnaA C-terminal domain IV

Domain ID domain_id	d2hcbc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

Domain ID domain_id	d2hcbd1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.12 — TrpR-like
Family Family family	a.4.12.2 — Chromosomal replication initiation factor DnaA C-terminal domain IV

Domain ID domain_id	d2hcbd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (12 domains)

Domain ID domain_id	2hcbA01
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	2hcbA02
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	2hcbA03
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	2hcbB01
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	2hcbB02
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	2hcbB03
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	2hcbC01
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	2hcbC02
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	2hcbC03
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	2hcbD01
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	2hcbD02
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	2hcbD03
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

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Unit-cell length a length_a	99.076 Å
Unit-cell length b length_b	117.714 Å
Unit-cell length c length_c	200.994 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	3.510 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2674
R_work r_work	0.2657
R_free r_free	0.2980

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

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

2hcb__assembly_1__model_1

2hcb__assembly_1__model_1 | I(q)

2hcb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Structure of AMPPCP-bound DnaA from Aquifex aeolicus

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

2hcb__assembly_1__model_1

2hcb__assembly_1__model_1 | I(q)

2hcb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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 non-polymer

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)