5c31

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

Method: X-RAY DIFFRACTION

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

Sin, putative plasmid resolvase dimer

Staphylococcus aureus

UniProt P20384

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 6 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 6 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 9 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIN3_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 1–128 Author chain B； PDBConstruct 1–128； UniProt 1–128 Author chain C； PDBConstruct 1–128； UniProt 1–128 Author chain D； PDBConstruct 1–128； UniProt 1–128 Author chain E； PDBConstruct 1–128； UniProt 1–128 Author chain F； PDBConstruct 1–128； UniProt 1–128 Author chain G； PDBConstruct 1–128； UniProt 1–128 Author chain H； PDBConstruct 1–128； UniProt 1–128 Author chain I； PDBConstruct 1–128； UniProt 1–128 Author chain J； PDBConstruct 1–128； UniProt 1–128 Author chain K； PDBConstruct 1–128； UniProt 1–128 Author chain L； PDBConstruct 1–128； UniProt 1–128

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	5c31
Deposition date deposition_date	2015-06-16
Structure title title	Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates
Keywords keywords	Serine recombinase, Site specific recombinase, Conformational flexibility, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

5c31__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5c31__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c31__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.63 Å
Rg (electron density)	24.60 Å
Total Rg	25.30 Å
Atom count	4595
Residues	474
Excluded volume	74119 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c31__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5c31__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5c31__assembly_3__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	Sin, putative plasmid resolvase dimer
Molecular weight formula_weight	15151.4 kDa
Mutation mutation	R54E, I113V
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	13750

MIIGYARVSSLDQNLERQLENLKTFGAEKIFTEKQSGKSIENRPILQKALNFVEMGDRFIVESIDRLGRNYNEVIHTVNYLKDKEVQLMITSLPMMNEVIGNPLLDKFMKDLVIQILAMVSEQERNES

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5c31a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31i_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31j_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31k_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

Domain ID domain_id	d5c31l_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.53 — Resolvase-like
Superfamily Superfamily superfamily	c.53.1 — Resolvase-like
Family Family family	c.53.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	5c31A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31I00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31J00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31K00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

Domain ID domain_id	5c31L00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1390 — Resolvase, N-terminal catalytic domain

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Unit-cell length a length_a	65.589 Å
Unit-cell length b length_b	152.719 Å
Unit-cell length c length_c	193.753 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	48

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	49.754 Å
R factor r_factor	0.2304
R_work r_work	0.2273
R_free r_free	0.2863

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

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

Sin, putative plasmid resolvase dimer

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

5c31__assembly_3__model_1

5c31__assembly_3__model_1 | I(q)

5c31__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Constitutively active Sin recombinase catalytic domain reveals two rotational intermediates

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

Sin, putative plasmid resolvase dimer

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

5c31__assembly_3__model_1

5c31__assembly_3__model_1 | I(q)

5c31__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)