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- PDB-2q66: Structure of Yeast Poly(A) Polymerase with ATP and oligo(A) -

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Basic information

Entry
Database: PDB / ID: 2q66
TitleStructure of Yeast Poly(A) Polymerase with ATP and oligo(A)
Components
  • 5'-R(P*AP*AP*AP*AP*A)-3'
  • Poly(A) polymerasePolynucleotide adenylyltransferase
KeywordsTransferase/RNA / protein RNA complex ATP polymerase complex / Transferase-RNA COMPLEX
Function / homology
Function and homology information


sno(s)RNA 3'-end processing / termination of RNA polymerase II transcription, poly(A)-coupled / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / : / 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
ADENOSINE-5'-TRIPHOSPHATE / RNA / Poly(A) polymerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBohm, A. / Balbo, P.
CitationJournal: Structure / Year: 2007
Title: Mechanism of poly(A) polymerase: structure of the enzyme-MgATP-RNA ternary complex and kinetic analysis.
Authors: Balbo, P.B. / Bohm, A.
History
DepositionJun 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: 5'-R(P*AP*AP*AP*AP*A)-3'
A: Poly(A) polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,18821
Polymers61,6012
Non-polymers1,58719
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.633, 85.907, 107.469
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain / Protein , 2 types, 2 molecules XA

#1: RNA chain 5'-R(P*AP*AP*AP*AP*A)-3'


Mass: 1601.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic
#2: Protein Poly(A) polymerase / Polynucleotide adenylyltransferase / PAP / Polynucleotide adenylyltransferase


Mass: 59999.840 Da / Num. of mol.: 1 / Mutation: D154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAP1 / Production host: Escherichia coli (E. coli)
References: UniProt: P29468, polynucleotide adenylyltransferase

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Non-polymers , 4 types, 528 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: .1M bis tris propane pH 6.4, .2M Li acetate, 16% Peg 3350, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Components of the solutions
IDNameCrystal-IDSol-ID
1bis tris propane11
2Li acetate11
3Peg11
4H2O11
5bis tris propane12
6Li acetate12
7Peg12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 56633 / % possible obs: 95.7 % / Redundancy: 12 % / Rmerge(I) obs: 0.072 / Χ2: 1.829 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.867.50.27544380.77776
1.86-1.9410.50.27550191.11386
1.94-2.0311.80.22155671.21795.2
2.03-2.1312.40.18157891.52999.3
2.13-2.2712.80.14958851.729100
2.27-2.4412.90.11858901.755100
2.44-2.6912.90.09259021.83100
2.69-3.0812.90.06959351.942100
3.08-3.8812.70.0659692.637100
3.88-30120.04962392.82299.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HHP

2hhp


Resolution: 1.8→29.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.642 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2896 5.1 %RANDOM
Rwork0.189 ---
obs0.191 56560 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.984 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 110 100 509 5049
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224663
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9996361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46524.434212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5811528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2712
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023469
X-RAY DIFFRACTIONr_nbd_refined0.1950.22454
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2442
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.239
X-RAY DIFFRACTIONr_mcbond_it0.8251.52793
X-RAY DIFFRACTIONr_mcangle_it1.12124417
X-RAY DIFFRACTIONr_scbond_it1.76232162
X-RAY DIFFRACTIONr_scangle_it2.5484.51914
LS refinement shellResolution: 1.8→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 139 -
Rwork0.267 2988 -
obs-3127 72.67 %

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