SAXSdb — 8amu

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

Replication protein RepB

Streptococcus agalactiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(TPCPGPGPCPGPAPCPTPTPTPTPCPGPGPCPGPAPCPTPTPTPT)-3') ; × 1 ;DNA (5'-D(APAPAPAPGPTPCPGPCPCPGPAPAPAPAPGPTPCPGPCPCPGPA)-3') ; × 1 MANGANESE (II) ION × 2 water × 3	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(TPCPGPGPCPGPAPCPTPTPTPTPCPGPGPCPGPAPCPTPTPTPT)-3') ; × 1 ;DNA (5'-D(APAPAPAPGPTPCPGPCPCPGPAPAPAPAPGPTPCPGPCPCPGPA)-3') ; × 1 MANGANESE (II) ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	REPB_STRAG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–140； UniProt 2–132 Author chain B； PDBConstruct 10–140； UniProt 2–132 Author chain E； PDBConstruct 10–140； UniProt 2–132 Author chain F； PDBConstruct 10–140； UniProt 2–132

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	8amu
Deposition date deposition_date	2022-08-04
Structure title title	RepB pMV158 OBD domain bound to DDR region
Keywords keywords	rolling circle replication, RepB, pMV158, DDR region, 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.

8amu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8amu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8amu__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.21 Å
Rg (electron density)	26.87 Å
Total Rg	27.53 Å
Atom count	3089
Residues	309
Excluded volume	52877 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8amu__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8amu__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Replication protein RepB
Molecular weight formula_weight	16413.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	6196

MKHHHHHHQAKEKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYV

Source Source

Source organism organism	Streptococcus agalactiae
NCBI taxonomy ID ncbi_taxonomy_id	1311
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPCPGPGPCPGPAPCPTPTPTPTPCPGPGPCPGPAPCPTPTPTP*T)-3') ;
Molecular weight formula_weight	7029.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,G

TCGGCGACTTTTCGGCGACTTTT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APAPAPAPGPTPCPGPCPCPGPAPAPAPAPGPTPCPGPCPCPGP*A)-3') ;
Molecular weight formula_weight	7092.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,H

AAAAGTCGCCGAAAAGTCGCCGA

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8amuA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	8amuB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	8amuE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	8amuF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1310 — Replication Protein E1; Chain: A,
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	49.234 Å
Unit-cell length b length_b	33.619 Å
Unit-cell length c length_c	289.672 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	24.690 Å
R factor r_factor	0.2298
R_work r_work	0.2270
R_free r_free	0.2818

RepB pMV158 OBD domain bound to DDR region

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

Replication protein RepB

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

8amu__assembly_2__model_1

8amu__assembly_2__model_1 | I(q)

8amu__assembly_2__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 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

RepB pMV158 OBD domain bound to DDR region

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

Replication protein RepB

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

8amu__assembly_2__model_1

8amu__assembly_2__model_1 | I(q)

8amu__assembly_2__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 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)