SAXSdb — 2p72

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

Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein

Paramecium bursaria Chlorella virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 URIDINE-5'-DIPHOSPHATE-GLUCOSE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q89399_PBCV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–213； UniProt 1–211 Author chain B； PDBConstruct 3–213； UniProt 1–211

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	2p72
Deposition date deposition_date	2007-03-19
Structure title title	crystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1
Keywords keywords	glycosyltransferase, PBCV-1, 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.

2p72__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2p72__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p72__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.00 Å
Rg (electron density)	15.87 Å
Total Rg	17.00 Å
Atom count	1747
Residues	204
Excluded volume	30948 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p72__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2p72__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 (4)

Entity 1 Entity 1 polymer

Description description	Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
Molecular weight formula_weight	25162.4 kDa
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	3555

ASMTTPCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCGTSRAERDEHMEMVAT

Source Source

Source organism organism	Paramecium bursaria Chlorella virus 1
NCBI taxonomy ID ncbi_taxonomy_id	10506
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
Molecular weight formula_weight	566.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2p72A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2p72B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	126.448 Å
Unit-cell length b length_b	61.776 Å
Unit-cell length c length_c	76.091 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2080
R_work r_work	0.2070
R_free r_free	0.2330

crystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1

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

Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein

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

2p72__assembly_2__model_1

2p72__assembly_2__model_1 | I(q)

2p72__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

crystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1

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

Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein

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

2p72__assembly_2__model_1

2p72__assembly_2__model_1 | I(q)

2p72__assembly_2__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)