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- PDB-2i7x: Structure of Yeast CPSF-100 (Ydh1p) -

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Basic information

Entry
Database: PDB / ID: 2i7x
TitleStructure of Yeast CPSF-100 (Ydh1p)
ComponentsProtein CFT2
KeywordsRNA BINDING PROTEIN / PROTEIN BINDING / polyadenylation / metallo-B-lactamase / pre-mRNA processing / Artemis / V(D)J recombination / double-strand break repair
Function / homology
Function and homology information


Processing of Intronless Pre-mRNAs / termination of RNA polymerase II transcription, poly(A)-coupled / mRNA cleavage and polyadenylation specificity factor complex / : / mRNA processing / RNA binding / nucleus
Similarity search - Function
Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Cleavage and polyadenylation specificity factor 2, C-terminal / CPSF2, metallo-hydrolase domain / Cleavage and polyadenylation factor 2 C-terminal / Cleavage and polyadenylation specificity factor subunit 2 / Rossmann fold - #10890 / Metallo-beta-lactamase superfamily domain / Beta-Casp domain / Beta-Casp domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cleavage factor two protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsMandel, C.R. / Zhang, H. / Gebauer, D. / Tong, L.
CitationJournal: Nature / Year: 2006
Title: Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease.
Authors: Mandel, C.R. / Kaneko, S. / Zhang, H. / Gebauer, D. / Vethantham, V. / Manley, J.L. / Tong, L.
History
DepositionAug 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 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 / Item: _software.classification / _software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CFT2


Theoretical massNumber of molelcules
Total (without water)80,6781
Polymers80,6781
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.631, 122.801, 126.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein CFT2 / Cleavage factor two protein 2 / 105 kDa protein associated with polyadenylation factor I


Mass: 80677.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CFT2, YDH1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q12102
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 1.82 Å3/Da / Density % sol: 32.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.2M ammonium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 20806 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.4674
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 5.644 / % possible all: 100

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Processing

Software
NameVersionClassification
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
PATSOLphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→28.18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 459366.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1905 9.8 %RANDOM
Rwork0.212 ---
obs0.212 19531 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.7429 Å2 / ksol: 0.301021 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1--13.94 Å20 Å20 Å2
2---3.62 Å20 Å2
3---17.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 0 148 4084
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.401 160 9.6 %
Rwork0.286 1511 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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