SAXSdb — 1vky

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

S-adenosylmethionine:tRNA ribosyltransferase-isomerase

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	UNKNOWN LIGAND × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	QUEA_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–347； UniProt 1–335 Author chain B； PDBConstruct 13–347； UniProt 1–335

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	1vky
Deposition date deposition_date	2004-06-28
Structure title title	Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution
Keywords keywords	;TM0574, S-adenosylmethionine tRNA ribosyltransferase, STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, ISOMERASE ;; ISOMERASE
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.

1vky__assembly_1__model_1

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

Download this curve (.dat)

1vky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vky__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.85 Å
Rg (electron density)	28.96 Å
Total Rg	29.74 Å
Atom count	4519
Residues	563
Excluded volume	81525 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vky__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	S-adenosylmethionine:tRNA ribosyltransferase-isomerase
Molecular weight formula_weight	40184.7 kDa
EC 编号 ec_number	5.-.-.-
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	4681

MGSDKIHHHHHHMKVSEFDYELPPELIAQEPVEPRDASRLMVLHRKTQRIEHRIFREIIEYLEPGDLLVLNVSKVIPARLYARKKTGASIEILLIERLEEGIWKCLVRPGQKVKKGTELVIDEDLSAVCLGRGEDGTRILKFQPQDDRLIFEKGRTPLPPYIKNEVPLERYQTVYAKEEGSVAAPTAGLHFTPELIEKLKKKGVQFAEVVLHVGIGTFRPVKVEEVEKHKMHEEFYQVPKETVRKLRETRERGNRIVAVGTTTVRTLETIARLPEQEEYVGKTDLFIYPPFEFKLVDALVTNFHLPRSTLLMLVAAFAGKDFVMEAYREAVKRRYRFFSFGDAMLIL

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	UNKNOWN LIGAND
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	162

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vkya_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.53 — QueA-like
Superfamily Superfamily superfamily	e.53.1 — QueA-like
Family Family family	e.53.1.1 — QueA-like

Domain ID domain_id	d1vkyb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.53 — QueA-like
Superfamily Superfamily superfamily	e.53.1 — QueA-like
Family Family family	e.53.1.1 — QueA-like

CATH v4.4 (4 domains)

Domain ID domain_id	1vkyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1780 — QueA-like
Homologous superfamily homologous superfamily	10 — QueA-like

Domain ID domain_id	1vkyA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	240 — QueA-like

Domain ID domain_id	1vkyB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1780 — QueA-like
Homologous superfamily homologous superfamily	10 — QueA-like

Domain ID domain_id	1vkyB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	240 — QueA-like

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Unit-cell length a length_a	119.033 Å
Unit-cell length b length_b	122.843 Å
Unit-cell length c length_c	131.207 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.390 Å
R factor r_factor	0.1811
R_work r_work	0.1795
R_free r_free	0.2104

Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution

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

S-adenosylmethionine:tRNA ribosyltransferase-isomerase

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

1vky__assembly_1__model_1

1vky__assembly_1__model_1 | I(q)

1vky__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of S-adenosylmethionine tRNA ribosyltransferase (TM0574) from Thermotoga maritima at 2.00 A resolution

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

S-adenosylmethionine:tRNA ribosyltransferase-isomerase

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

1vky__assembly_1__model_1

1vky__assembly_1__model_1 | I(q)

1vky__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)