SAXSdb — 1ydx

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

type I restriction enzyme specificity protein MG438

Mycoplasma genitalium

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	T1SX_MYCGE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–406； UniProt 1–383

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	1ydx
Deposition date deposition_date	2004-12-27
Structure title title	Crystal structure of Type-I restriction-modification system S subunit from M. genitalium
Keywords keywords	TYPE-I HSDS, 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.

1ydx__assembly_1__model_1

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

Download this curve (.dat)

1ydx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ydx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.94 Å
Rg (electron density)	27.08 Å
Total Rg	28.03 Å
Atom count	3034
Residues	368
Excluded volume	54590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ydx__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	type I restriction enzyme specificity protein MG438
Molecular weight formula_weight	47276.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3163

MGHHHHHHHHHHSSGHIDDDDKHMTPKLKLNNNINWTKRTIDSLFDLKKGEMLEKELITPEGKYEYFNGGVKNSGRTDKFNTFKNTISVIVGGSCGYVRLADKNFFCGQSNCTLNLLDPLELDLKFAYYALKSQQERIEALAFGTTIQNIRISDLKELEIPFTSNKNEQHAIANTLSVFDERLENLASLIEINRKLRDEYAHKLFSLDEAFLSHWKLEALQSQMHEITLGEIFNFKSGKYLKSEERLEEGKFPYYGAGIDNTGFVAEPNTEKDTISIISNGYSLGNIRYHEIPWFNGTGSIALEPMNNEIYVPFFYCALKYLQKDIKERMKSDDSPFLSLKLAGEIKVPYVKSFQLQRKAGKIVFLLDQKLDQYKKELSSLTVIRDTLLKKLFPDMTERTKSIKDY

Source Source

Source organism organism	Mycoplasma genitalium
NCBI taxonomy ID ncbi_taxonomy_id	2097
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	129

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ydxa1
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	d1ydxa2
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 (3 domains)

Domain ID domain_id	1ydxA01
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	1ydxA02
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	1ydxA03
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	76.601 Å
Unit-cell length b length_b	76.601 Å
Unit-cell length c length_c	174.847 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1988
R_work r_work	0.1970
R_free r_free	0.2313

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

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

type I restriction enzyme specificity protein MG438

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

1ydx__assembly_1__model_1

1ydx__assembly_1__model_1 | I(q)

1ydx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Type-I restriction-modification system S subunit from M. genitalium

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

type I restriction enzyme specificity protein MG438

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

1ydx__assembly_1__model_1

1ydx__assembly_1__model_1 | I(q)

1ydx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)