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- PDB-2o1p: Structure of yeast Poly(A) Polymerase in a somewhat closed state -

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Basic information

Entry
Database: PDB / ID: 2o1p
TitleStructure of yeast Poly(A) Polymerase in a somewhat closed state
ComponentsPoly(A) polymerasePolynucleotide adenylyltransferase
KeywordsTRANSFERASE / poly(A) polymerase
Function / homology
Function and homology information


termination of RNA polymerase II transcription, poly(A)-coupled / sno(s)RNA 3'-end processing / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / mRNA 3'-end processing / : / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBohm, A. / Balbo, P. / Toth, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase.
Authors: Balbo, P.B. / Toth, J. / Bohm, A.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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
B: Poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)125,2482
Polymers125,2482
Non-polymers00
Water3,297183
1
A: Poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,6241
Polymers62,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(A) polymerase


Theoretical massNumber of molelcules
Total (without water)62,6241
Polymers62,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.217, 108.587, 132.718
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 / Polynucleotide adenylyltransferase / PAP / Polynucleotide adenylyltransferase


Mass: 62623.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAP1 / Plasmid: Pet21b / Production host: Escherichia coli (E. coli)
References: UniProt: P29468, polynucleotide adenylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% Peg 8000 100mM magnesium acetate 100mM imidazole pH 6.2 3% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2005
RadiationMonochromator: X25 Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→84 Å / Num. all: 31888 / Num. obs: 31665 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.105 / Net I/σ(I): 16.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.2 / Num. unique all: 4216 / Rsym value: 0.334 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FA0

1fa0


Resolution: 2.7→65.51 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.866 / SU B: 27.941 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27508 1664 5 %RANDOM
Rwork0.19499 ---
obs0.19892 31665 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.7→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 0 183 8532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228536
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.94811567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57924.118391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.926151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0181553
X-RAY DIFFRACTIONr_chiral_restr0.0910.21297
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026423
X-RAY DIFFRACTIONr_nbd_refined0.2130.23789
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2286
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.210
X-RAY DIFFRACTIONr_mcbond_it0.4761.55360
X-RAY DIFFRACTIONr_mcangle_it0.83228479
X-RAY DIFFRACTIONr_scbond_it1.21633582
X-RAY DIFFRACTIONr_scangle_it1.9634.53088
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 135 -
Rwork0.265 2287 -
obs--99.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6460.0966-0.80324.68681.25021.95710.1049-0.11730.1522-0.274-0.061-0.0738-0.11440.0195-0.0439-0.18310.0452-0.0219-0.03230.0135-0.00865.77457.70730.56
21.2734-0.39170.06743.8046-0.25711.6662-0.01140.0305-0.037-0.0951-0.09150.24930.1312-0.01760.1028-0.22950.01230.0048-0.0787-0.06860.062858.33929.13331.989
33.7161.0068-0.36645.78960.78262.94850.3333-0.4650.51841.3357-0.02670.3222-0.29640.1376-0.30660.2953-0.10520.2542-0.0138-0.0988-0.063459.87937.38562.594
42.12840.6202-0.02126.22542.38972.5181-0.0313-0.02440.2188-1.01380.14-0.4068-0.52290.2165-0.10870.0419-0.00730.065-0.0890.0524-0.073628.84585.99377.586
51.4477-0.0797-0.0242.9937-0.64381.46790.07130.0577-0.0728-0.51870.04240.11070.0954-0.0353-0.1137-0.0607-0.0063-0.0787-0.08470.0073-0.081420.3857.32878.469
63.1227-1.36310.16016.0410.72172.5319-0.1049-0.35670.33030.99360.1729-0.4011-0.2620.1097-0.06790.0409-0.0559-0.0461-0.0215-0.0215-0.099123.39364.12109.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA41 - 19041 - 190
2X-RAY DIFFRACTION2AA4 - 404 - 40
3X-RAY DIFFRACTION2AA191 - 357191 - 357
4X-RAY DIFFRACTION3AA358 - 532358 - 532
5X-RAY DIFFRACTION4BB41 - 19041 - 190
6X-RAY DIFFRACTION5BB3 - 403 - 40
7X-RAY DIFFRACTION5BB191 - 357191 - 357
8X-RAY DIFFRACTION6BB358 - 528358 - 528

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