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- PDB-3ef0: The Structure of Fcp1, an essential RNA polymerase II CTD phosphatase -

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Basic information

Entry
Database: PDB / ID: 3ef0
TitleThe Structure of Fcp1, an essential RNA polymerase II CTD phosphatase
ComponentsRNA polymerase II subunit A C-terminal domain phosphatase
KeywordsHYDROLASE / phosphatase / CTD / FCPH / BRCT / AlF4 / transition state analog / Cobalt / Magnesium / Manganese / Metal-binding / Nucleus / Protein phosphatase
Function / homology
Function and homology information


Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / RNA polymerase II CTD heptapeptide repeat phosphatase activity / signaling / myosin phosphatase activity / protein-serine/threonine phosphatase / metal ion binding / nucleus
Similarity search - Function
FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / twin BRCT domain / BRCT domain / S15/NS1, RNA-binding ...FCP1-like phosphatase, phosphatase domain / CTD phosphatase Fcp1 / CTD small RNA polymerase II polypeptide A phosphatase-like / FCP1 homology domain / NLI interacting factor-like phosphatase / FCP1 homology domain profile. / catalytic domain of ctd-like phosphatases / twin BRCT domain / BRCT domain / S15/NS1, RNA-binding / HAD superfamily/HAD-like / BRCT domain profile. / BRCT domain / BRCT domain superfamily / HAD superfamily / HAD-like superfamily / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / RNA polymerase II subunit A C-terminal domain phosphatase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGhosh, A. / Lima, C.D.
CitationJournal: Mol.Cell / Year: 2008
Title: The structure of Fcp1, an essential RNA polymerase II CTD phosphatase.
Authors: Ghosh, A. / Shuman, S. / Lima, C.D.
History
DepositionSep 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 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: RNA polymerase II subunit A C-terminal domain phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5113
Polymers42,3831
Non-polymers1272
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.169, 80.682, 89.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA polymerase II subunit A C-terminal domain phosphatase / / CTD phosphatase fcp1


Mass: 42383.434 Da / Num. of mol.: 1
Fragment: FCP1 homology domain, Catalytically active fragment, UNP residues 149-580
Source method: isolated from a genetically manipulated source
Details: leaves behind N-termiminal SL
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: fcp1, SPAC19B12.05c / Plasmid: TOPO-adapted pET28b-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus
References: UniProt: Q9P376, protein-serine/threonine phosphatase
#2: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP Q9P376 RESIDUES 330-393 ARE DELETED AND REPLACED BY RESIDUES 'SG'

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Fcp1-AlF4--Mg was obtained by incubating 250 M Fcp1(149-580)- 330-393 with 500 M AlCl3, 5 mM NaF and 5 mM MgCl2 on ice for 2 h prior to crystallization by hanging drop vapor diffusion ...Details: Fcp1-AlF4--Mg was obtained by incubating 250 M Fcp1(149-580)- 330-393 with 500 M AlCl3, 5 mM NaF and 5 mM MgCl2 on ice for 2 h prior to crystallization by hanging drop vapor diffusion against 20% PEG-3350, 190 mM ammonium formate (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23771 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.069 / Χ2: 1.162 / Net I/σ(I): 25.159
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 5 / Num. unique all: 2312 / Χ2: 0.79 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementStarting model: Fcp1-BeF3-Mg model

Resolution: 2.1→30 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1680323 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1189 5 %RANDOM
Rwork0.22 ---
all-23973 --
obs-23733 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.769 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 100.41 Å2 / Biso mean: 33.948 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1-6.52 Å20 Å20 Å2
2---1.71 Å20 Å2
3----4.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-30 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 6 175 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it3.82.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 195 5.1 %
Rwork0.244 3660 -
all-3855 -
obs--98.4 %
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
X-RAY DIFFRACTION5alf.paralf.top

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