SAXSdb — 3eey

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

Putative rRNA methylase

Clostridium thermocellum ATCC 27405

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 SULFATE ION × 4 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 2 SULFATE ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 2 GLYCEROL × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 2 GLYCEROL × 1 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	S-ADENOSYLMETHIONINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3DDA2_CLOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–189； UniProt 3–188 Author chain B； PDBConstruct 4–189； UniProt 3–188 Author chain C； PDBConstruct 4–189； UniProt 3–188 Author chain D； PDBConstruct 4–189； UniProt 3–188 Author chain E； PDBConstruct 4–189； UniProt 3–188 Author chain F； PDBConstruct 4–189； UniProt 3–188 Author chain G； PDBConstruct 4–189； UniProt 3–188 Author chain H； PDBConstruct 4–189； UniProt 3–188 Author chain I； PDBConstruct 4–189； UniProt 3–188 Author chain J； PDBConstruct 4–189； UniProt 3–188

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	3eey
Deposition date deposition_date	2008-09-06
Structure title title	CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum
Keywords keywords	;RRNA METHYLATION, S-ADENOSYL-METHIONINE, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM, NYSGXRC, METHYLTRANSFERASE, TRANSFERASE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS ;; 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.

3eey__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3eey__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eey__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	24.15 Å
Rg (electron density)	23.00 Å
Total Rg	23.81 Å
Atom count	2864
Residues	368
Excluded volume	51450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eey__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3eey__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3eey__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3eey__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3eey__assembly_5__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	Putative rRNA methylase
Molecular weight formula_weight	21838.0 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	15399

MSLTIKNSLGQSHDYIKMFVKEGDTVVDATCGNGNDTAFLASLVGENGRVFGFDIQDKAIANTTKKLTDLNLIDRVTLIKDGHQNMDKYIDCPVKAVMFNLGYLPSGDHSISTRPETTIQALSKAMELLVTGGIITVVIYYGGDTGFEEKEKVLEFLKGVDQKKFIVQRTDFINQANCPPILVCIEKISEGHHHHHH

Source Source

Source organism organism	Clostridium thermocellum ATCC 27405
NCBI taxonomy ID ncbi_taxonomy_id	203119
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	9

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	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3eeyA00
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	3eeyB00
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	3eeyC00
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	3eeyD00
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	3eeyE00
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	3eeyF00
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	3eeyG00
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	3eeyH00
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	3eeyI00
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	3eeyJ00
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

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Unit-cell length a length_a	70.156 Å
Unit-cell length b length_b	126.913 Å
Unit-cell length c length_c	125.611 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2447
R_work r_work	0.2436
R_free r_free	0.2784

CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum

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

Putative rRNA methylase

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

3eey__assembly_5__model_1

3eey__assembly_5__model_1 | I(q)

3eey__assembly_5__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF PUTATIVE RRNA-METHYLASE FROM Clostridium thermocellum

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

Putative rRNA methylase

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

3eey__assembly_5__model_1

3eey__assembly_5__model_1 | I(q)

3eey__assembly_5__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) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)