SAXSdb — 3grv

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

Dimethyladenosine transferase

Methanocaldococcus jannaschii

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KSGA_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–295； UniProt 1–275

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	3grv
Deposition date deposition_date	2009-03-26
Structure title title	Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1
Keywords keywords	;DimethylAdenosine Transferase, Rossmann fold, Ribosomal Assembly S-Adenosyl-L-Methionine, RRNA, Methyltransferase, RNA-binding, rRNA processing, S-adenosyl-L-methionine, 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.

3grv__assembly_1__model_1

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

Download this curve (.dat)

3grv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3grv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.20 Å
Rg (electron density)	21.44 Å
Total Rg	22.23 Å
Atom count	2119
Residues	262
Excluded volume	38118 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3grv__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 (4)

Entity 1 Entity 1 polymer

Description description	Dimethyladenosine transferase
Molecular weight formula_weight	33877.3 kDa
EC 编号 ec_number	2.1.1.-
Mutation mutation	K137A,E138A
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	2365

MGSSHHHHHHSSGLVPRGSHMFKPKKKLGQCFLIDKNFVNKAVESANLTKDDVVLEIGLGKGILTEELAKNAKKVYVIEIDKSLEPYANKLKELYNNIEIIWGDALKVDLNKLDFNKVVANLPYQISSPITFKLIKRGFDLAVLMYQYEFAKRMVAAAGTKDYGRLSVAVQSRADVEIVAKVPPSAFYPKPKVYSAIVKIKPNKGKYHIENENFFDDFLRAIFQHRNKSVRKALIDSSKELNYNKDEMKKILEDFLNTNSEIKNLINEKVFKLSVKDIVNLSNEFYRFLQNRGRL

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE
Molecular weight formula_weight	267.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3grva_
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.66.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3grvA01
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	3grvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	100 — rRNA adenine dimethylase, C-terminal domain

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Unit-cell length a length_a	40.263 Å
Unit-cell length b length_b	66.018 Å
Unit-cell length c length_c	61.691 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	22.000 Å
R factor r_factor	0.1827
R_work r_work	0.1797
R_free r_free	0.2392

Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1

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

Dimethyladenosine transferase

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

3grv__assembly_1__model_1

3grv__assembly_1__model_1 | I(q)

3grv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1

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

Dimethyladenosine transferase

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

3grv__assembly_1__model_1

3grv__assembly_1__model_1 | I(q)

3grv__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)