SAXSdb — 3dcm

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

Uncharacterized protein TM_1570

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	S-ADENOSYLMETHIONINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1570_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–192； UniProt 1–192

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	3dcm
Deposition date deposition_date	2008-06-04
Structure title title	Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine
Keywords keywords	Trefoil knot, SPOUT Mtase, AdoMet binding, 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.

3dcm__assembly_1__model_1

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

Download this curve (.dat)

3dcm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dcm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.72 Å
Rg (electron density)	20.51 Å
Total Rg	21.42 Å
Atom count	3084
Residues	376
Excluded volume	55348 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dcm__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Uncharacterized protein TM_1570
Molecular weight formula_weight	22008.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	1670

MLEKVYVALIHYPIKGKDGSIISTAVTNLDVHDIARTARTYNLKGYYIVTNLRAQQDMVSKMLKFWREGFGSRYNPSRAESLKLVKLKSYLEDVLEDIESVEGERPLIFFTSAKKRENDISFEEGRRIIIETEKPVLILLGTGWGLPDEILEISDYVLEPIRAQSDFNHLSVRAAAAIIIDRLIGENYARRD

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	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3dcmX00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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Unit-cell length a length_a	79.648 Å
Unit-cell length b length_b	63.402 Å
Unit-cell length c length_c	54.522 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	129.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	17.430 Å
R factor r_factor	0.2010
R_work r_work	0.1980
R_free r_free	0.2350

Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine

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

Uncharacterized protein TM_1570

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

3dcm__assembly_1__model_1

3dcm__assembly_1__model_1 | I(q)

3dcm__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the Thermotoga maritima SPOUT family RNA-methyltransferase protein Tm1570 in complex with S-adenosyl-L-methionine

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

Uncharacterized protein TM_1570

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

3dcm__assembly_1__model_1

3dcm__assembly_1__model_1 | I(q)

3dcm__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)