SAXSdb — 8amv

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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 homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 6 SODIUM ION × 1 water × 5	Consistent with protein count

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 1–210； UniProt 1–210 Author chain B； PDBConstruct 1–210； UniProt 1–210 Author chain C； PDBConstruct 1–210； UniProt 1–210 Author chain D； PDBConstruct 1–210； UniProt 1–210 Author chain E； PDBConstruct 1–210； UniProt 1–210 Author chain F； PDBConstruct 1–210； UniProt 1–210

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	8amv
Deposition date deposition_date	2022-08-04
Structure title title	RepB pMV158 hexamer
Keywords keywords	rolling circle replication, RepB, pMV158, 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.

8amv__assembly_1__model_1

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

Download this curve (.dat)

8amv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8amv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.37 Å
Rg (electron density)	36.70 Å
Total Rg	37.22 Å
Atom count	9564
Residues	1169
Excluded volume	173250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8amv__assembly_1__model_1`	hexameric （6）	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 (4)

Entity 1 Entity 1 polymer

Description description	Replication protein RepB
Molecular weight formula_weight	24287.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	9615

MAKEKARYFTFLLYPESIPSDWELKLETLGVPMAISPLHDKDKSSIKGQKYKKAHYHVLYIAKNPVTADSVRKKIKLLLGEKSLAMVQVVLNVENMYLYLTHESKDAIAKKKHVYDKADIKLINNFDIDRYVTLDVEEKTELFNVVVSLIRAYTLQNIFDLYDFIDENGETYGLTINLVNEVIAGKTGFMKLLFDGAYQRSKRGTKNEER

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 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	8amvB01
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	8amvB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1480 — Plasmid replication protein

Domain ID domain_id	8amvC01
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	8amvC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1480 — Plasmid replication protein

Domain ID domain_id	8amvD01
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	8amvD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1480 — Plasmid replication protein

Domain ID domain_id	8amvE01
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	8amvE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1480 — Plasmid replication protein

Domain ID domain_id	8amvF01
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	8amvF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1480 — Plasmid replication protein

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Unit-cell length a length_a	90.910 Å
Unit-cell length b length_b	79.330 Å
Unit-cell length c length_c	114.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.92 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	45.480 Å
R factor r_factor	0.2206
R_work r_work	0.2182
R_free r_free	0.2671

RepB pMV158 hexamer

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

8amv__assembly_1__model_1

8amv__assembly_1__model_1 | I(q)

8amv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

RepB pMV158 hexamer

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

8amv__assembly_1__model_1

8amv__assembly_1__model_1 | I(q)

8amv__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)