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- PDB-2p51: Crystal structure of the S. pombe Pop2p deadenylation subunit -

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Basic information

Entry
Database: PDB / ID: 2p51
TitleCrystal structure of the S. pombe Pop2p deadenylation subunit
ComponentsSPCC18.06c protein
KeywordsHYDROLASE / GENE REGULATION / DEDD nuclease fold
Function / homology
Function and homology information


poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / CCR4-NOT complex / : / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / RNA nuclease activity / P-body / manganese ion binding ...poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / CCR4-NOT complex / : / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / RNA nuclease activity / P-body / manganese ion binding / mRNA binding / chromatin binding / zinc ion binding / metal ion binding / nucleus / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(A) ribonuclease pop2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.4 Å
AuthorsThyssen Jonstrup, A. / Andersen, K.R. / Van, L.B. / Brodersen, D.E.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme
Authors: Thyssen Jonstrup, A. / Andersen, K.R. / Van, L.B. / Brodersen, D.E.
History
DepositionMar 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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: SPCC18.06c protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3663
Polymers37,3171
Non-polymers492
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.370, 54.089, 90.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe single molecule in the asu constitutes the biological assembly

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Components

#1: Protein SPCC18.06c protein


Mass: 37316.930 Da / Num. of mol.: 1 / Fragment: POP2P DEADENYLATION SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC18.06c (caf1 homologue) / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O74856
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 6.9262 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18-24% PEG 8000, 200 mM Mg(CH3COO), 100-200 mM MES, pH 6.5, 0-10% glycerol, 5 mM BME, 1mM NaN3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 10, 2005 / Details: Bent, vertically focussing mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
Reflection

D res high: 2.2 Å / D res low: 99 Å

IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
118.7623890.0822.221234782.7
219.3985630.0811.141502199.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.749999.710.0592.25
3.764.7410010.0762.616
3.293.7610010.092.495
2.993.2999.910.1172.165
2.772.9999.510.141.975
2.612.7797.110.1591.864
2.482.6189.310.1741.703
2.372.4873.310.1821.478
2.282.3745.910.2081.4
2.22.2817.610.1970.95
4.749999.320.0621.065
3.764.7499.820.0671.048
3.293.7699.920.0771.174
2.993.2910020.0891.266
2.772.9910020.0971.236
2.612.7710020.1061.21
2.482.6110020.1191.176
2.372.4810020.1321.144
2.282.3799.920.1431.036
2.22.2898.220.1530.944
ReflectionResolution: 1.4→46.47 Å / Num. all: 50856 / Num. obs: 50856 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.311 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.174 / Net I/σ(I): 26.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.98 / Num. unique all: 2489 / Χ2: 1.026 / % possible all: 99.7

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
SHELXrefinement
PDB_EXTRACT2data extraction
SHELXL-97refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.4→46.47 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1523 3 %RANDOM
Rwork0.139 ---
all0.143 50856 --
obs0.141 50856 99.6 %-
Displacement parametersBiso mean: 23.937 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 2 327 2413
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_from_restr_planes0.359
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.066
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
1.4-1.52X-RAY DIFFRACTION10179544.69
1.52-1.67X-RAY DIFFRACTION9525564.34
1.67-1.92X-RAY DIFFRACTION10033578.44
1.92-2.42X-RAY DIFFRACTION9696590.98
2.42-46.47X-RAY DIFFRACTION9737591.84

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