5x06

DNA replication regulation protein

Method: X-RAY DIFFRACTION

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

DNA polymerase III subunit beta

Escherichia coli O157:H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DnaA regulatory inactivator Hda × 4 （P69933） GLYCEROL × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPO3B_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–386； UniProt 1–366 Author chain B； PDBConstruct 21–386； UniProt 1–366 Author chain C； PDBConstruct 21–386； UniProt 1–366 Author chain D； PDBConstruct 21–386； UniProt 1–366

DnaA regulatory inactivator Hda

Escherichia coli O157:H7

UniProt P69933

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA polymerase III subunit beta × 4 （P0A990） GLYCEROL × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HDA_ECO57
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 21–253； UniProt 1–233 Author chain F； PDBConstruct 21–253； UniProt 1–233 Author chain G； PDBConstruct 21–253； UniProt 1–233 Author chain H； PDBConstruct 21–253； UniProt 1–233

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	5x06
Deposition date deposition_date	2017-01-20
Structure title title	DNA replication regulation protein
Keywords keywords	DNA replication, RIDA, 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.

5x06__assembly_1__model_1

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

Download this curve (.dat)

5x06__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5x06__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.83 Å
Rg (electron density)	51.19 Å
Total Rg	51.47 Å
Atom count	18234
Residues	2300
Excluded volume	324640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5x06__assembly_1__model_1`	octameric （8）	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 (6)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III subunit beta
Molecular weight formula_weight	42801.9 kDa
EC 编号 ec_number	2.7.7.7
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	18264

MGSSHHHHHHSSGLVPRGSHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DnaA regulatory inactivator Hda
Molecular weight formula_weight	28835.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MGSSHHHHHHSSGLVPRGSHMNTPAQLSLPLYLPDDETFASFWPGDNSSLLAALQNVLRQEHSGYIYLWAREGAGRSHLLHAACAELSQRGDAVGYVPLDKRTWFVPEVLDGMEHLSLVCIDNIECIAGDELWEMAIFDLYNRILESGKTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEDKLQALQLRARLRGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQRKLTIPFVKEILKL

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5x06A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06A03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06B01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06B02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06B03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06C01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06C02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06C03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06D01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06D02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	5x06D03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

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Unit-cell length a length_a	102.112 Å
Unit-cell length b length_b	149.542 Å
Unit-cell length c length_c	200.780 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	3.237 Å
Low-resolution limit resolution_low	40.593 Å
R factor r_factor	0.2277
R_work r_work	0.2257
R_free r_free	0.2653

DNA replication regulation protein

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

DNA polymerase III subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

DnaA regulatory inactivator Hda

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

5x06__assembly_1__model_1

5x06__assembly_1__model_1 | I(q)

5x06__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

DNA replication regulation protein

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

DNA polymerase III subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DnaA regulatory inactivator Hda

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

5x06__assembly_1__model_1

5x06__assembly_1__model_1 | I(q)

5x06__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)