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- PDB-3owg: Crystal structure of vaccinia virus Polyadenylate polymerase(vp55) -

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Basic information

Entry
Database: PDB / ID: 3owg
TitleCrystal structure of vaccinia virus Polyadenylate polymerase(vp55)
ComponentsPoly(A) polymerase catalytic subunit
KeywordsTRANSFERASE / RNA polyadenylate polymerase complex / translocation / polyadenylate polymerase
Function / homology
Function and homology information


polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA processing / ATP binding / metal ion binding
Similarity search - Function
Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain ...Poxvirus poly(A) polymerase, N domain / Poxvirus poly(A) polymerase, nucleotidyltransferase domain / Poly(A) polymerase catalytic subunit, Poxviridae / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase, catalytic subunit, C-terminal / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal / Poly(A) polymerase catalytic subunit superfamily / Poxvirus poly(A) polymerase, catalytic subunit, N-terminal domain superfamily / Poxvirus poly(A) polymerase, nucleotidyltransferase domain superfamily / Poxvirus poly(A) polymerase nucleotidyltransferase domain / Poxvirus poly(A) polymerase C-terminal domain / Poxvirus poly(A) polymerase N-terminal domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Beta Polymerase; domain 2 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Poly(A) polymerase catalytic subunit
Similarity search - Component
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsLi, C. / Li, H. / Zhou, S. / Gershon, P.D. / Poulos, T.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Domain-level rocking motion within a polymerase that translocates on single-stranded nucleic acid.
Authors: Li, H. / Li, C. / Zhou, S. / Poulos, T.L. / Gershon, P.D.
#1: Journal: Mol.Cell / Year: 2006
Title: Crystal structures of the vaccinia virus polyadenylate polymerase heterodimer: insights into ATP selectivity and processivity.
Authors: Moure, C.M. / Bowman, B.R. / Gershon, P.D. / Quiocho, F.A.
#2: Journal: Structure / Year: 2009
Title: Polymerase translocation with respect to single-stranded nucleic acid: looping or wrapping of primer around a poly(A) polymerase.
Authors: Li, C. / Li, H. / Zhou, S. / Sun, E. / Yoshizawa, J. / Poulos, T.L. / Gershon, P.D.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(A) polymerase catalytic subunit
B: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)112,8062
Polymers112,8062
Non-polymers00
Water00
1
A: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)56,4031
Polymers56,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)56,4031
Polymers56,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.128, 161.290, 97.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Poly(A) polymerase catalytic subunit / Poly(A) polymerase large subunit / PAP-L / VP55


Mass: 56403.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Strain: Western Reserve / Gene: PAPL, VACWR057, E1L / Plasmid: pPG198 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P23371, polynucleotide adenylyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 12-16%PEG 3350,200mM Na-citate, 5% glycero, 1mM DTT, pH ~9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 29731 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 90 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2 / Rsym value: 0.577 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GA9

2ga9


Resolution: 2.86→41.77 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1227549.9 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED THE NCS RESTRAINTS (WEIGHT=100)WAS IMPOSED DURING REFINEMENTS
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1465 4.9 %RANDOM
Rwork0.253 ---
obs0.253 29693 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.8296 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 97.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.93 Å20 Å20 Å2
2---12.17 Å20 Å2
3----2.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.86→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 0 0 7436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
Refine LS restraints NCSNCS model details: RESTRAINT
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 222 5.1 %
Rwork0.365 4153 -
obs-4153 88.6 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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