SAXSdb — 3bgy

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

;Polynucleotide 5'-triphosphatase ;

Acanthamoeba polyphaga mimivirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCE_MIMIV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 1–237 Author chain B； PDBConstruct 1–237； UniProt 1–237

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	3bgy
Deposition date deposition_date	2007-11-27
Structure title title	Triclinic structure of Mimivirus Capping Enzyme Triphosphatase at 1.65 A
Keywords keywords	;RNA capping, Tunnel Triphsophatase, Metalloenzyme, Beta Barrel, Hydrolase, mRNA capping, mRNA processing, Multifunctional enzyme, Nucleotidyltransferase, S-adenosyl-L-methionine, Transferase, Virion, VIRAL PROTEIN ;; HYDROLASE, VIRAL PROTEIN
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.

3bgy__assembly_1__model_1

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

Download this curve (.dat)

3bgy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bgy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.69 Å
Rg (electron density)	18.64 Å
Total Rg	19.64 Å
Atom count	1857
Residues	226
Excluded volume	33218 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bgy__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bgy__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	;Polynucleotide 5'-triphosphatase ;
Molecular weight formula_weight	27560.3 kDa
EC 编号 ec_number	3.1.3.33
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	4514

MGTKLKKSNNDITIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD

Source Source

Source organism organism	Acanthamoeba polyphaga mimivirus
NCBI taxonomy ID ncbi_taxonomy_id	212035
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	580

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3bgyA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

Domain ID domain_id	3bgyB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

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Unit-cell length a length_a	39.640 Å
Unit-cell length b length_b	48.460 Å
Unit-cell length c length_c	69.700 Å
Unit-cell angle α angle_alpha	74.62 °
Unit-cell angle β angle_beta	86.48 °
Unit-cell angle γ angle_gamma	76.36 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	33.830 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2120

Triclinic structure of Mimivirus Capping Enzyme Triphosphatase at 1.65 A

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

;Polynucleotide 5'-triphosphatase ;

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

3bgy__assembly_1__model_1

3bgy__assembly_1__model_1 | I(q)

3bgy__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Triclinic structure of Mimivirus Capping Enzyme Triphosphatase at 1.65 A

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

;Polynucleotide 5'-triphosphatase ;

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

3bgy__assembly_1__model_1

3bgy__assembly_1__model_1 | I(q)

3bgy__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)