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- PDB-2bf0: crystal structure of the rpr of pcf11 -

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Basic information

Entry
Database: PDB / ID: 2bf0
Titlecrystal structure of the rpr of pcf11
ComponentsPCF11
KeywordsTRANSCRIPTION / RNA / PHOSPHORYLATION
Function / homology
Function and homology information


termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / mRNA cleavage factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / RNA polymerase II complex binding / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / Protein PCF11-like / CID domain / RPR ...: / Pfc11 Rna14/15 interacting domain / Subunit of cleavage factor IA Pcf11, C-terminal / : / : / Pcf11, Clp1-interaction domain / Pcf11, C-terminal domain / Protein PCF11-like / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsNoble, C.G. / Hollingworth, D. / Martin, S.R. / Adeniran, V.E. / Smerdon, S.J. / Kelly, G. / Taylor, I.A. / Ramos, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Key Features of the Interaction between Pcf11 Cid and RNA Polymerase II Ctd.
Authors: Noble, C.G. / Hollingworth, D. / Martin, S.R. / Adeniran, V.E. / Smerdon, S.J. / Kelly, G. / Taylor, I.A. / Ramos, A.
History
DepositionDec 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.pdbx_leaving_atom_flag / _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
X: PCF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6742
Polymers16,6341
Non-polymers401
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.494, 75.494, 56.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PCF11


Mass: 16633.701 Da / Num. of mol.: 1 / Fragment: CID, RESIDUES 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39081
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.8
Details: 25% PEG 4000, 0.1 M TRIS PH 7.0, 0.2 M (NH4)2SO4 AND 10 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976,0.9792,0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.97921
30.97951
ReflectionResolution: 2.3→20 Å / Num. obs: 7191 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 36

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.282 350 4.6 %RANDOM
Rwork0.258 ---
obs0.26 7191 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2---1.52 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 1 56 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.9721482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.83130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02806
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.3576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.573
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.316
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9070.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8011.5659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50721071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2433439
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8184.5411
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.481 21
Rwork0.244 525

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