SAXSdb — 1yf2

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

Type I restriction-modification enzyme, S subunit

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y130_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–425； UniProt 1–425 Author chain B； PDBConstruct 1–425； UniProt 1–425

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	1yf2
Deposition date deposition_date	2004-12-30
Structure title title	Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications
Keywords keywords	;Type I restriction modification enzyme, S-subunit, Structural genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, HYDROLASE REGULATOR ;; HYDROLASE REGULATOR
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.

1yf2__assembly_2__model_1

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

Download this curve (.dat)

1yf2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yf2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.61 Å
Rg (electron density)	28.70 Å
Total Rg	29.47 Å
Atom count	3416
Residues	425
Excluded volume	62167 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yf2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yf2__assembly_2__model_1`	monomeric （1）	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 (2)

Entity 1 Entity 1 polymer

Description description	Type I restriction-modification enzyme, S subunit
Molecular weight formula_weight	48639.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7157

MFYKEENFKKTEIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITNSNKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIPKDNILESEFLYYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILTKIDEGIEIIEKSINKLERIKKGLMHKLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQKQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLTGKVRVKT

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	243232
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	329

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yf2a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.287 — DNA methylase specificity domain
Superfamily Superfamily superfamily	d.287.1 — DNA methylase specificity domain
Family Family family	d.287.1.2 — Type I restriction modification DNA specificity domain

Domain ID domain_id	d1yf2a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.287 — DNA methylase specificity domain
Superfamily Superfamily superfamily	d.287.1 — DNA methylase specificity domain
Family Family family	d.287.1.2 — Type I restriction modification DNA specificity domain

Domain ID domain_id	d1yf2b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.287 — DNA methylase specificity domain
Superfamily Superfamily superfamily	d.287.1 — DNA methylase specificity domain
Family Family family	d.287.1.2 — Type I restriction modification DNA specificity domain

Domain ID domain_id	d1yf2b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.287 — DNA methylase specificity domain
Superfamily Superfamily superfamily	d.287.1 — DNA methylase specificity domain
Family Family family	d.287.1.2 — Type I restriction modification DNA specificity domain

CATH v4.4 (6 domains)

Domain ID domain_id	1yf2A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

Domain ID domain_id	1yf2A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1120 — Bipartite methylase S protein

Domain ID domain_id	1yf2A03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

Domain ID domain_id	1yf2B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

Domain ID domain_id	1yf2B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1120 — Bipartite methylase S protein

Domain ID domain_id	1yf2B03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2
Homologous superfamily homologous superfamily	20 — DNA methylase specificity domains

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Unit-cell length a length_a	71.972 Å
Unit-cell length b length_b	94.222 Å
Unit-cell length c length_c	103.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.520 Å
R factor r_factor	0.2360
R_work r_work	0.2360
R_free r_free	0.2790

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

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

Type I restriction-modification enzyme, S subunit

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

1yf2__assembly_2__model_1

1yf2__assembly_2__model_1 | I(q)

1yf2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

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

Type I restriction-modification enzyme, S subunit

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

1yf2__assembly_2__model_1

1yf2__assembly_2__model_1 | I(q)

1yf2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)