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3owg

Crystal structure of vaccinia virus Polyadenylate polymerase(vp55)

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Poly(A) polymerase catalytic subunit

Vaccinia virus WR

UniProt P23371

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–479 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.86 Å R-free 0.316
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–479 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.86 Å R-free 0.316

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.

Other PDB Difference from Current Entry 3OWG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GA9 Crystal Structure of the Heterodimeric Vaccinia Virus Polyadenylate Polymerase with Bound ATP-gamma-S Deposited 2006-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 11–479（469 aa）
Mutation：L36S CA CALCIUM ION × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.240 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.260
2GAF Crystal Structure of the Vaccinia Polyadenylate Polymerase Heterodimer (apo form) Deposited 2006-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 11–479（469 aa）
Mutation：L36S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；20% PEG 4000, 0.24 M CaCl2, 5% glycerol, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.288
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain D 1–479（479 aa）
Mutation：L36S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.18 Å R-free 0.285
3ER8 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with two fragments of RNA Deposited 2008-10-01 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 1–479（479 aa）
Mutation：L36S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.18 Å R-free 0.285
3ER9 Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase complex with UU and 3'-deoxy ATP Deposited 2008-10-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain B 1–479（479 aa）
Mutation：L36S GOL GLYCEROL × 3 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；proteins(4-5mg.ml) in 10mM tris-HCl, pH 8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.06 Å R-free 0.250
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain D 1–479（479 aa）
Mutation：L36S U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.21 Å R-free 0.309
3ERC Crystal structure of the heterodimeric vaccinia virus mRNA polyadenylate polymerase with three fragments of RNA and 3'-deoxy ATP Deposited 2008-10-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 1–479（479 aa）
Mutation：L36S U5P URIDINE-5'-MONOPHOSPHATE × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.7；295 K；Proteins(4-5mg.ml) in 10mM Tris-HCl, pH8.7, 75 mM NaCl, 0.5 mM DTT, mixed with equal volume buffer which composed of 10mM Tris-HCl, pH 8.7, 15-20% PEG 4000, 5% glycerol, 0.5 mM DTT. Room temperature for several days., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 3.21 Å R-free 0.309

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAP1_VACCW
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–485； UniProt 1–479 Author chain B； PDBConstruct 7–485； UniProt 1–479

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 3owg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3owg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3owg
Deposition date deposition_date2010-09-17
Structure title titleCrystal structure of vaccinia virus Polyadenylate polymerase(vp55)
Keywords keywordsRNA polyadenylate polymerase complex, translocation, polyadenylate polymerase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.09 Å
Radius of gyration Rg (electron density) rg_electron33.81 Å
Forward intensity I(0) i0164278000.00
Molecular weight molecular_weight105960.0 kDa
Excluded volume excluded_volume134100 ų
Envelope volume envelope_volume168850 ų
Hydration-shell volume shell_volume42408 ų
Envelope diameter envelope_diameter128.5 Å
Shell Rg shell_rg39.74 Å
Envelope Rg envelope_rg33.54 Å
Shape Rg shape_rg33.81 Å
Total Rg total_rg34.24 Å
Total atoms total_atoms7436
Residues n_residues914
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.2 Å
Rg (real space) rg_real34.09 Å
Rg uncertainty (real space) rg_real_error1.10 Å
I(0) (real space) i0_real1.6430e+08
I(0) uncertainty (real space) i0_real_error2.8290e+06
Rg (reciprocal space) rg_reciprocal34.10 Å
I(0) (reciprocal space) i0_reciprocal164300000.0000
Solution quality estimate total_estimate0.8748
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9 Å
Skewness Skewness skewness0.316
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54080000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.954
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3owga_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.69 — Poly(A) polymerase catalytic subunit-like
Superfamily Superfamily superfamilye.69.1 — Poly(A) polymerase catalytic subunit-like
Family Family familye.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like
Domain ID domain_idd3owgb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.69 — Poly(A) polymerase catalytic subunit-like
Superfamily Superfamily superfamilye.69.1 — Poly(A) polymerase catalytic subunit-like
Family Family familye.69.1.1 — Poxvirus poly(A) polymerase catalytic subunit-like

CATH v4.4 (4 domains)

Domain ID domain_id3owgA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily320 — Poxvirus poly(A) polymerase, N domain
Domain ID domain_id3owgA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain
Domain ID domain_id3owgB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily320 — Poxvirus poly(A) polymerase, N domain
Domain ID domain_id3owgB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily60 — Poxvirus poly(A) polymerase, nucleotidyltransferase domain
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8. Citations (3)

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9. Files and Curves (10)