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- PDB-1q78: Crystal structure of poly(A) polymerase in complex with 3'-dATP a... -

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Basic information

Entry
Database: PDB / ID: 1q78
TitleCrystal structure of poly(A) polymerase in complex with 3'-dATP and magnesium chloride
ComponentsPoly(A) polymerase alpha
KeywordsTRANSFERASE / mRNA processing / nucleotidyl transferase
Function / homology
Function and homology information


mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / : / manganese ion binding / magnesium ion binding ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Processing of Intronless Pre-mRNAs / Processing of Capped Intron-Containing Pre-mRNA / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / : / manganese ion binding / magnesium ion binding / RNA binding / ATP binding / nucleus
Similarity search - Function
Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...Poly(A) polymerase / : / Poly(A) polymerase nucleotidyltransferase domain / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(a)-polymerase, middle domain - #10 / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / Poly(A) polymerase alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsMartin, G. / Moglich, A. / Keller, W. / Doublie, S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Biochemical and structural insights into substrate binding and catalytic mechanism of mammalian poly(A) polymerase.
Authors: Martin, G. / Moglich, A. / Keller, W. / Doublie, S.
History
DepositionAug 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(A) polymerase alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7313
Polymers59,2151
Non-polymers5152
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.520, 63.810, 180.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(A) polymerase alpha / PAP / Polynucleotide adenylyltransferase alpha


Mass: 59215.305 Da / Num. of mol.: 1 / Fragment: residues 1-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PAPOLA OR PAP / Plasmid: pGM10 BovPAP513 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P25500, polynucleotide adenylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, Ammonium sulfate, MES buffer, calcium chloride, magnesium chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 15989 / Num. obs: 15770 / % possible obs: 92.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.7 Å2
Reflection shellResolution: 2.8→2.97 Å / % possible all: 64.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.76 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1004 6.4 %RANDOM
Rwork0.204 ---
all0.204 15989 --
obs0.204 15770 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8214 Å2 / ksol: 0.320059 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.23 Å20 Å20 Å2
2--8.98 Å20 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 31 123 3950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it1.832
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 113 6.3 %
Rwork0.308 1688 -
obs--64.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5HETERO-CPDS-MR.PARHETERO-CPDS-MR.TOP

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