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- PDB-1sz9: The RNA polymerase II CTD in mRNA processing: beta-turn recogniti... -

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Basic information

Entry
Database: PDB / ID: 1sz9
TitleThe RNA polymerase II CTD in mRNA processing: beta-turn recognition and beta-spiral model
ComponentsPCF11 protein
KeywordsTRANSCRIPTION / Pcf11 / RNA polymerase II CTD interacting domain / arm repeats
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 / termination of RNA polymerase II transcription / : / RNA polymerase II complex binding / mRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / Pcf11, Clp1-interaction domain / CID domain / RPR / CID domain / CID domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS ...Subunit of cleavage factor IA Pcf11, C-terminal / Protein PCF11-like / : / Pcf11, Clp1-interaction domain / 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 / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMeinhart, A. / Cramer, P.
CitationJournal: Nature / Year: 2004
Title: Recognition of RNA polymerase II carboxy-terminal domain by 3'-RNA-processing factors.
Authors: Meinhart, A. / Cramer, P.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PCF11 protein
B: PCF11 protein
C: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)49,8723
Polymers49,8723
Non-polymers00
Water1,964109
1
A: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)16,6241
Polymers16,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)16,6241
Polymers16,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PCF11 protein


Theoretical massNumber of molelcules
Total (without water)16,6241
Polymers16,6241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.730, 67.670, 135.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PCF11 protein


Mass: 16624.145 Da / Num. of mol.: 3 / Fragment: CTD interacting domain of Pcf11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PCF11, YDR228C, YD9934.13C / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P39081
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 25 % (v/v) ethylene glycol, 5 % (v/v) PEG 550, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 29988 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rsym value: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.2 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.307 / % possible all: 96.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
CNSrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: ORIGINAL MODEL FROM MAD EXPERIMENT WAS USED FOR FURTHER REFINEMENT. R-FREE SET WAS KEPT CONSISTEND

Resolution: 2.1→20 Å / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1400 4.5 %RANDOM
Rwork0.22 ---
obs0.22 29988 98 %-
all-31174 --
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 0 109 3570
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.211
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.569
X-RAY DIFFRACTIONc_mcangle_it2.405
X-RAY DIFFRACTIONc_scbond_it2.439
X-RAY DIFFRACTIONc_scangle_it3.515
LS refinement shellResolution: 2.1→2.13 Å / Total num. of bins used: 28 /
RfactorNum. reflection
Rfree0.256 16
Rwork0.225 406

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