SAXSdb — 2r72

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

INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE

Infectious bursal disease virus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDRP_IBDV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–852； UniProt 1–845

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	2r72
Deposition date deposition_date	2007-09-07
Structure title title	Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.
Keywords keywords	IBDV, infectious bursal disease virus, birnavirus, VP1, polymerase, magnesium, mg, 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.

2r72__assembly_1__model_1

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

Download this curve (.dat)

2r72__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r72__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.51 Å
Rg (electron density)	27.45 Å
Total Rg	28.32 Å
Atom count	5918
Residues	765
Excluded volume	105900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r72__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 (3)

Entity 1 Entity 1 polymer

Description description	INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE
Molecular weight formula_weight	94651.9 kDa
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	5921

GSRSTVSMSDVFNSPQARSTISAAFGIKPTAGQDVEELLIPKVWVPPEDPLASPSRLAKFLRENGYKVLQPRSLPENEEYETDQILPDLAWMRQIEGAVLKPTLSLPIGDQEYFPKYYPTHRPSKEKPNAYPPDIALLKQMIYLFLQVPEANEGLKDEVTLLTQNIRDKAYGSGTYMGQANRLVAMKEVATGRNPNKDPLKLGYTFESIAQLLDITLPVGPPGEDDKPWVPLTRVPSRMLVLTGDVDGDFEVEDYLPKINLKSSSGLPYVGRTKGETIGEMIAISNQFLRELSTLLKQGAGTKGSNKKKLLSMLSDYWYLSCGLLFPKAERYDKSTWLTKTRNIWSAPSPTHLMISMITWPVMSNSPNNVLNIEGCPSLYKFNPFRGGLNRIVEWILAPEEPKALVYADNIYIVHSNTWYSIDLEKGEANCTRQHMQAAMYYILTRGWSDNGDPMFNQTWATFAMNIAPALVVDSSCLIMNLQIKTYGQGSGNAATFINNHLLSTLVLDQWNLMRQPRPDSEEFKSIEDKLGINFKIERSIDDIRGKLRQLVLLAQPGYLSGGVEPEQSSPTVELDLLGWSATYSKDLGIYVPVLDKERLFCSAAYPKGVENKSLKSKVGIEQAYKVVRYEALRLVGGWNYPLLNKACKNNAGAARRHLEAKGFPLDEFLAEWSELSEFGEAFEGFNIKLTVTSESLAELNKPVPPKPPNVNRPVNTGGLKAVSNALKTGRYRNEAGLSGLVLLATARSRLQDAVKAKAEAEKLHKSKPDDPDADWFERSETLSDLLEKADIASKVAHSALVETSDALEAVQSTSVYTPKYPEVKNPQTASNPVVGLHLPAKRATGVQAALL

Source Source

Source organism organism	Infectious bursal disease virus
Common name common_name	Gumboro virus
NCBI taxonomy ID ncbi_taxonomy_id	10995
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2r72a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2r72A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1730 — Infectious bursal virus vp1 polymerase fold
Homologous superfamily homologous superfamily	10 — Infectious bursal virus vp1 polymerase domain

Domain ID domain_id	2r72A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	540 — Helix hairpin bin

Domain ID domain_id	2r72A04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2r72A05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	80 —

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Unit-cell length a length_a	122.838 Å
Unit-cell length b length_b	122.838 Å
Unit-cell length c length_c	354.255 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.150 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2110
R_work r_work	0.2090
R_free r_free	0.2350

Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.

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

INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE

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

2r72__assembly_1__model_1

2r72__assembly_1__model_1 | I(q)

2r72__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) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.

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

INFECTIOUS BURSAL DISEASE VIRUS VP1 POLYMERASE

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

2r72__assembly_1__model_1

2r72__assembly_1__model_1 | I(q)

2r72__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) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (1)