SAXSdb — 3gyq

▼

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

;rRNA (adenosine-2'-O-)-methyltransferase ;

Streptomyces cyaneus

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	TSNR_STRCN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–272； UniProt 1–269 Author chain B； PDBConstruct 4–272； UniProt 1–269

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3gyq
Deposition date deposition_date	2009-04-04
Structure title title	Structure of the Thiostrepton-Resistance Methyltransferase S-adenosyl-L-methionine Complex
Keywords keywords	;rRNA Methyltransferase, SPOUT MTases, SAM, Trefoil knot, Antibiotic resistance, Methyltransferase, S-adenosyl-L-methionine, Transferase ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3gyq__assembly_1__model_1

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

Download this curve (.dat)

3gyq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gyq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.78 Å
Rg (electron density)	24.67 Å
Total Rg	25.48 Å
Atom count	3976
Residues	522
Excluded volume	70832 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gyq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	;rRNA (adenosine-2'-O-)-methyltransferase ;
Molecular weight formula_weight	29215.3 kDa
EC 编号 ec_number	2.1.1.66
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	4048

GSHMTELDTIANPSDPAVQRIIDVTKPSRSNIKTTLIEDVEPLMHSIAAGVEFIEVYGSDSSPFPSELLDLCGRQNIPVRLIDSSIVNQLFKGERKAKTFGIARVPRPARFGDIASRRGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIADRRLQRASRGYVFSLPVVLSGREEAIAFIRDSGMQLMTLKADGDISVKELGDNPDRLALLFGSEKGGPSDLFEEASSASVSIPMMSQTESLNVSVSLGIALHERIDRNLAANR

Source Source

Source organism organism	Streptomyces cyaneus
Common name common_name	Streptomyces curacoi
NCBI taxonomy ID ncbi_taxonomy_id	1904
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	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	72

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3gyqA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	3gyqA02
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

Domain ID domain_id	3gyqB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	3gyqB02
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

▶

Unit-cell length a length_a	40.960 Å
Unit-cell length b length_b	55.770 Å
Unit-cell length c length_c	215.580 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	19.388 Å
R factor r_factor	0.2180
R_work r_work	0.2150
R_free r_free	0.2680

Structure of the Thiostrepton-Resistance Methyltransferase S-adenosyl-L-methionine Complex

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

;rRNA (adenosine-2'-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

3gyq__assembly_1__model_1

3gyq__assembly_1__model_1 | I(q)

3gyq__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the Thiostrepton-Resistance Methyltransferase S-adenosyl-L-methionine Complex

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

;rRNA (adenosine-2'-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

3gyq__assembly_1__model_1

3gyq__assembly_1__model_1 | I(q)

3gyq__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)