2vp3

DC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG

Method: X-RAY DIFFRACTION Dmax: 62.7 Å Quality: GOOD

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

VP39

Vaccinia virus

UniProt P07617

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–307 Mutation:26 C-TERMINAL RESIDUES DELETED SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;DC26/ADOHCY CRYSTAL SOAKED IN 10MM M7GDP., pH 6.5 Resolution 1.95 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAP2_VACCV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 16–322; UniProt 1–307

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2vp3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2vp3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2vp3
Deposition date deposition_date1996-12-16
Structure title titleDC26 MUTANT OF VACCINIA VIRUS PROTEIN VP39 IN COMPLEX WITH S-ADENOSYLHOMOCYSTEINE AND M7G(5')PPPG
Keywords keywordsMETHYLTRANSFERASE, RNA CAP, POLY(A) POLYMERASE, VACCINIA, MRNA PROCESSING, TRANSCRIPTION; METHYLTRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.13
Radius of gyration Rg (electron density) rg_electron19.01
Forward intensity I(0) i019447800.00
Molecular weight molecular_weight34859.0 kDa
Excluded volume excluded_volume44163 ų
Envelope volume envelope_volume49740 ų
Hydration-shell volume shell_volume21375 ų
Envelope diameter envelope_diameter63.5
Shell Rg shell_rg25.76
Envelope Rg envelope_rg19.24
Shape Rg shape_rg19.01
Total Rg total_rg19.93
Total atoms total_atoms2457
Residues n_residues291
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax62.7
Rg (real space) rg_real20.01
Rg uncertainty (real space) rg_real_error0.28
I(0) (real space) i0_real1.9450e+07
I(0) uncertainty (real space) i0_real_error2.2440e+05
Rg (reciprocal space) rg_reciprocal20.03
I(0) (reciprocal space) i0_reciprocal19450000.0000
Solution quality estimate total_estimate0.8973
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.8
Skewness Skewness skewness0.127
Kurtosis Kurtosis kurtosis-0.491
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5530000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.991

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2vp3a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamilyc.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family familyc.66.1.25 — mRNA cap methylase

CATH v4.4 (1 domains)

Domain ID domain_id2vp3A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39

8. Citations (2)

9. Files and Curves (10)