SAXSdb — 1dl5

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

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CADMIUM ION × 9 CHLORIDE ION × 10 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CADMIUM ION × 9 CHLORIDE ION × 10 S-ADENOSYL-L-HOMOCYSTEINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PIMT_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317

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	1dl5
Deposition date deposition_date	1999-12-08
Structure title title	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
Keywords keywords	METHYLTRANSFERASE, ISOASPARTYL RESIDUES, PROTEIN REPAIR, DEAMIDATION, POST-TRANSLATIONAL MODIFICATION, TRANSFERASE; TRANSFERASE
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.

1dl5__assembly_1__model_1

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

Download this curve (.dat)

1dl5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dl5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.33 Å
Rg (electron density)	33.98 Å
Total Rg	34.05 Å
Atom count	5167
Residues	633
Excluded volume	92937 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dl5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dl5__assembly_2__model_1`	dimeric （2）	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	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE
Molecular weight formula_weight	36440.8 kDa
EC 编号 ec_number	2.1.1.77
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	5640

MREKLFWILKKYGVSDHIAKAFLEIPREEFLTKSYPLSYVYEDIVLVSYDDGEEYSTSSQPSLMALFMEWVGLDKGMRVLEIGGGTGYNAAVMSRVVGEKGLVVSVEYSRKICEIAKRNVERLGIENVIFVCGDGYYGVPEFSPYDVIFVTVGVDEVPETWFTQLKEGGRVIVPINLKLSRRQPAFLFKKKDPYLVGNYKLETRFITAGGNLGNLLERNRKLLREFPFNREILLVRSHIFVELVDLLTRRLTEIDGTFYYAGPNGVVEFLDDRMRIYGDAPEIENLLTQWESCGYRSFEYLMLHVGYNAFSHISCSI

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dl5a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.7 — Protein-L-isoaspartyl O-methyltransferase

Domain ID domain_id	d1dl5a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.197 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Superfamily Superfamily superfamily	d.197.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Family Family family	d.197.1.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

Domain ID domain_id	d1dl5b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.7 — Protein-L-isoaspartyl O-methyltransferase

Domain ID domain_id	d1dl5b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.197 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Superfamily Superfamily superfamily	d.197.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain
Family Family family	d.197.1.1 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1dl5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dl5A02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	20 — Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

Domain ID domain_id	1dl5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

Domain ID domain_id	1dl5B02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	20 — Protein-l-isoaspartate O-methyltransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Protein-L-isoaspartyl O-methyltransferase, C-terminal domain

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Unit-cell length a length_a	51.060 Å
Unit-cell length b length_b	98.910 Å
Unit-cell length c length_c	76.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.66 °
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	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2030

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

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

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

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

1dl5__assembly_1__model_1

1dl5__assembly_1__model_1 | I(q)

1dl5__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

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

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

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

1dl5__assembly_1__model_1

1dl5__assembly_1__model_1 | I(q)

1dl5__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)