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- PDB-4wse: Crystal structure of the Mimivirus polyadenylate synthase -

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Basic information

Entry
Database: PDB / ID: 4wse
TitleCrystal structure of the Mimivirus polyadenylate synthase
ComponentsPutative poly(A) polymerase catalytic subunit
KeywordsTRANSFERASE / PolyA polymerase
Function / homologyPoly(A) polymerase catalytic subunit / : / virion component => GO:0044423 / polynucleotide adenylyltransferase / mRNA processing / ATP binding / Putative poly(A) polymerase catalytic subunit
Function and homology information
Biological speciesAcanthamoeba polyphaga mimivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsPriet, S. / Lartigue, A. / Claverie, J.M. / Abergel, C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: mRNA maturation in giant viruses: variation on a theme.
Authors: Priet, S. / Lartigue, A. / Debart, F. / Claverie, J.M. / Abergel, C.
History
DepositionOct 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative poly(A) polymerase catalytic subunit
B: Putative poly(A) polymerase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)136,6612
Polymers136,6612
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-36 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.030, 69.650, 97.490
Angle α, β, γ (deg.)90.000, 105.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative poly(A) polymerase catalytic subunit


Mass: 68330.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R341 / Plasmid: modified pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta
References: UniProt: Q5UQS6, polynucleotide adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG 400, imidazole

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97887 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 2.84→46.01 Å / Num. obs: 30587 / % possible obs: 99.4 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.049 / Net I/σ(I): 10.3 / Num. measured all: 127445
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.84-2.913.90.6991.8875722380.8120.499.1
12.7-46.013.50.04232.213143740.9980.02496.9

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Processing

Software
NameVersionClassification
XDSdata reduction
BUSTER-TNT2.10.2refinement
Aimless0.3.6data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P37

4p37


Resolution: 2.84→46.01 Å / Cor.coef. Fo:Fc: 0.8601 / Cor.coef. Fo:Fc free: 0.8663 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.392
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1521 4.97 %RANDOM
Rwork0.2269 ---
obs0.229 30587 99.31 %-
Displacement parametersBiso max: 208.19 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-35.4367 Å20 Å21.4539 Å2
2---64.4105 Å20 Å2
3---28.9738 Å2
Refine analyzeLuzzati coordinate error obs: 0.547 Å
Refinement stepCycle: final / Resolution: 2.84→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8257 0 0 240 8497
Biso mean---67.87 -
Num. residues----990
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3014SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes243HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1186HARMONIC5
X-RAY DIFFRACTIONt_it8457HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1103SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9996SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8457HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11424HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion22.43
LS refinement shellResolution: 2.84→2.94 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3627 159 5.33 %
Rwork0.2973 2825 -
all0.3008 2984 -
obs--99.31 %

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