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- PDB-1fa0: STRUCTURE OF YEAST POLY(A) POLYMERASE BOUND TO MANGANATE AND 3'-DATP -

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Basic information

Entry
Database: PDB / ID: 1fa0
TitleSTRUCTURE OF YEAST POLY(A) POLYMERASE BOUND TO MANGANATE AND 3'-DATP
ComponentsPOLY(A)-POLYMERASE
KeywordsTRANSFERASE / Polymerase / Nucleotidyl Transferase
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
3'-DEOXYADENOSINE / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / : / PYROPHOSPHATE 2- / Poly(A) polymerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsBard, J. / Zhelkovsky, A.M. / Helmling, S. / Moore, C.L. / Bohm, A.
CitationJournal: Science / Year: 2000
Title: Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP.
Authors: Bard, J. / Zhelkovsky, A.M. / Helmling, S. / Earnest, T.N. / Moore, C.L. / Bohm, A.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,76011
Polymers122,8792
Non-polymers1,8819
Water1,47782
1
A: POLY(A)-POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4686
Polymers61,4401
Non-polymers1,0285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POLY(A)-POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2925
Polymers61,4401
Non-polymers8524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.800, 109.100, 238.500
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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Protein , 1 types, 2 molecules AB

#1: Protein POLY(A)-POLYMERASE


Mass: 61439.508 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PJDELTA10PAP / Production host: Escherichia coli (E. coli)
References: UniProt: P29468, polynucleotide adenylyltransferase

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Non-polymers , 5 types, 91 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Chemical ChemComp-3AD / 3'-DEOXYADENOSINE / Cordycepin


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.91 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.24
Details: PEG,Ethylene Glycol, pH 7.24, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113.5 %ethylene glycol1reservoir
29 %PEG80001reservoir
36 %glycerol1reservoir
4100 mMHEPES1reservoir
52 mMdithiothreitol1reservoir
635 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: OTHER / Detector: CCD / Date: Feb 4, 2000
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 59680 / Num. obs: 58367 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.14 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 32.36
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.307 / Num. unique all: 7379 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 242159
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1052123.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 5098 8.5 %RANDOM
Rwork0.233 ---
obs0.233 50383 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso mean: 62.7 Å2
Baniso -1Baniso -2Baniso -3
1--20.26 Å20 Å20 Å2
2--10.19 Å20 Å2
3---10.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.73 Å0.69 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.19 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8061 0 109 82 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it2.172.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3443 300 9.7 %
Rwork0.3112 3075 -
obs--52.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CORD_POP.PARCORD_POP.TOP
X-RAY DIFFRACTION5DNA-RNA_REP_C2ENDORNA.PARDNA-RNA.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 8.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 62.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
% reflection Rfree: 9.7 %

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