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- PDB-4p37: Crystal structure of the Megavirus polyadenylate synthase -

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Basic information

Entry
Database: PDB / ID: 4p37
TitleCrystal structure of the Megavirus polyadenylate synthase
Components(Putative poly(A) polymerase catalytic ...) x 2
KeywordsTRANSFERASE / PolyA polymerase
Function / homology
Function and homology information


polynucleotide adenylyltransferase / virion component / mRNA processing / transferase activity
Similarity search - Function
Poly(A) polymerase catalytic subunit / : / Poly(A) polymerase catalytic subunit / APMV, Putative poly(A) polymerase, catalytic subunit, C-terminal
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative poly(A) polymerase catalytic subunit
Similarity search - Component
Biological speciesMegavirus chiliensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.24 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
DepositionMar 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,74416
Polymers127,3742
Non-polymers1,37014
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-6 kcal/mol
Surface area47880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.689, 96.132, 153.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsGel filtration confirms the dimerization of the protein in solution

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Components

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Putative poly(A) polymerase catalytic ... , 2 types, 2 molecules AB

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


Mass: 63666.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megavirus chiliensis / Gene: mg561 / Plasmid: modified pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: G5CT11
#2: Protein Putative poly(A) polymerase catalytic subunit


Mass: 63707.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megavirus chiliensis / Gene: mg561 / Plasmid: modified pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: G5CT11

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Non-polymers , 4 types, 592 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1M Tris-HCl, PEG 200

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793, 0.9795, 0.9770
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.9771
ReflectionResolution: 2.24→51.3 Å / Num. obs: 62550 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 49.16 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.7
Reflection shellResolution: 2.24→2.36 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.5 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.24→49.38 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.255 / SU Rfree Blow DPI: 0.184 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 3136 5.08 %RANDOM
Rwork0.1873 ---
obs0.1887 61727 98.7 %-
Displacement parametersBiso mean: 55.14 Å2
Baniso -1Baniso -2Baniso -3
1--14.2144 Å20 Å20 Å2
2--13.2862 Å20 Å2
3---0.9281 Å2
Refine analyzeLuzzati coordinate error obs: 0.276 Å
Refinement stepCycle: LAST / Resolution: 2.24→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8283 0 90 578 8951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098564HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0111513HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3097SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes225HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1191HARMONIC5
X-RAY DIFFRACTIONt_it8564HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion17.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1105SEMIHARMONIC5
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_contact9898SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2486 223 4.96 %
Rwork0.2203 4277 -
all0.2217 4500 -
obs--98.7 %

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