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- PDB-1uoc: X-ray structure of the RNase domain of the yeast Pop2 protein -

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Basic information

Entry
Database: PDB / ID: 1uoc
TitleX-ray structure of the RNase domain of the yeast Pop2 protein
ComponentsPOP2
KeywordsHYDROLASE / DEDD NUCLEASE / MRNA DEGRADATION / POLY(A) TAIL / TRANSCRIPTION REGULATION / REPRESSOR / PHOSPHORYLATION.
Function / homology
Function and homology information


poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / : / mating projection tip / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / 3'-5'-RNA exonuclease activity ...poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / : / mating projection tip / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / P-body / 3'-5'-RNA exonuclease activity / RNA binding / nucleus / metal ion binding / cytoplasm
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
XENON / Poly(A) ribonuclease POP2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsThore, S. / Mauxion, F. / Seraphin, B. / Suck, D.
CitationJournal: Embo Rep. / Year: 2003
Title: X-Ray Structure and Activity of the Yeast Pop2 Protein: A Nuclease Subunit of the Mrna Deadenylase Complex
Authors: Thore, S. / Mauxion, F. / Seraphin, B. / Suck, D.
History
DepositionSep 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POP2
B: POP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0326
Polymers66,6892
Non-polymers3434
Water81145
1
A: POP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5163
Polymers33,3451
Non-polymers1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: POP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5163
Polymers33,3451
Non-polymers1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.582, 79.440, 101.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.15744, -0.98751, -0.00592), (0.98753, -0.15744, -0.00114), (0.00019, -0.00602, 0.99998)
Vector: 72.15511, -55.78834, 25.1445)

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Components

#1: Protein POP2 / CCR4-ASSOCIATED FACTOR 1


Mass: 33344.594 Da / Num. of mol.: 2 / Fragment: RNASE D DOMAIN, RESIDUES 147-433
Source method: isolated from a genetically manipulated source
Details: 2 RESIDUES ADDED IN N-TERMINAL BECAUSE OF A TEV CLEAVABLE TAG.
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P39008
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Compound detailsUBIQUITOUS TRANSCRIPTION FACTOR. PART OF A GLUCOSE- SENSING SYSTEM INVOLVED IN GROWTH CONTROL.

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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: 2.65 Å3/Da / Density % sol: 53.2 %
Crystal growpH: 7.2
Details: 2.5% PEG 3350,100MM HEPES(PH7.0) 80MM CALCIUM ACETATE,16.5% GLYCEROL, pH 7.20
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 %PEG3350MW1reservoir
2100 mMHEPES1reservoirpH7.0
380 mMcalcium acetate1reservoir
416.5 %glycerol1reservoir
520 mMTris-Cl1droppH7.5
6200 mM1dropNaCl
79 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.84
DetectorDate: Feb 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.84 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 52320 / % possible obs: 95.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.9 / % possible all: 76.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 76.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→9.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1438159.75 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2589 5 %RANDOM
Rwork0.239 ---
obs0.239 51486 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.16 Å2 / ksol: 0.479404 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.68 Å20 Å20 Å2
2---6.62 Å20 Å2
3---1.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 4 45 4263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 208 5.4 %
Rwork0.327 3675 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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