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- PDB-4xpz: Structure of fission yeast RNA polymerase II CTD phosphatase Fcp1... -

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Basic information

Entry
Database: PDB / ID: 4xpz
TitleStructure of fission yeast RNA polymerase II CTD phosphatase Fcp1-R271A bound to aluminum fluoride
ComponentsRNA polymerase II subunit A C-terminal domain phosphatase
KeywordsHYDROLASE / Phosphatase / PolII-CTD / Transition state / AlF3
Function / homology
Function and homology information


Formation of the Early Elongation Complex / RNA Polymerase II Transcription Elongation / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / RNA polymerase II CTD heptapeptide repeat phosphatase activity / signaling / dephosphorylation of RNA polymerase II C-terminal domain / protein-serine/threonine phosphatase / metal ion binding / nucleus
Similarity search - Function
CTD phosphatase Fcp1 / FCP1-like phosphatase, phosphatase domain / CTD small RNA polymerase II polypeptide A phosphatase-like / catalytic domain of ctd-like phosphatases / FCP1 homology domain profile. / NLI interacting factor-like phosphatase / FCP1 homology domain / twin BRCT domain / BRCT domain / S15/NS1, RNA-binding ...CTD phosphatase Fcp1 / FCP1-like phosphatase, phosphatase domain / CTD small RNA polymerase II polypeptide A phosphatase-like / catalytic domain of ctd-like phosphatases / FCP1 homology domain profile. / NLI interacting factor-like phosphatase / FCP1 homology domain / 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
ALUMINUM FLUORIDE / RNA polymerase II subunit A C-terminal domain phosphatase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
Model detailsStructure of a Fcp1 mutant (R271A) in complex with AlF3 and Mg
AuthorsGhosh, A. / Lima, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM061906 United States
CitationJournal: Rna / Year: 2015
Title: Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1.
Authors: Schwer, B. / Ghosh, A. / Sanchez, A.M. / Lima, C.D. / Shuman, S.
History
DepositionJan 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)42,7945
Polymers42,2971
Non-polymers4974
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-3 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.692, 79.989, 89.132
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: 42297.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: fcp1, SPAC19B12.05c / Plasmid: TOPO-adapted pET28b-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL
References: UniProt: Q9P376, protein-serine/threonine phosphatase
#2: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 35% PEG-550MME and 100 mM MES

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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: Oct 11, 2008
RadiationMonochromator: Cryogenically-cooled double crystal Si(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 70713 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 1.2 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EF0
Resolution: 1.45→19.512 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 16.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 3549 5.07 %Random selection
Rwork0.1537 66518 --
obs0.1551 70067 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.57 Å2 / Biso mean: 26.6959 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: final / Resolution: 1.45→19.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 28 398 3325
Biso mean--45.2 38.47 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183132
X-RAY DIFFRACTIONf_angle_d1.564248
X-RAY DIFFRACTIONf_chiral_restr0.098476
X-RAY DIFFRACTIONf_plane_restr0.009548
X-RAY DIFFRACTIONf_dihedral_angle_d13.6561223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4501-1.470.28431470.26722609275698
1.47-1.4910.28611410.2412574271597
1.491-1.51320.2411430.22642602274598
1.5132-1.53690.26431490.21382640278998
1.5369-1.5620.21051190.20752619273899
1.562-1.5890.20391360.18942663279998
1.589-1.61780.24571300.18612638276899
1.6178-1.64890.23471500.17492631278199
1.6489-1.68260.1911520.17042652280499
1.6826-1.71920.19341520.16342620277299
1.7192-1.75910.20121410.15912678281999
1.7591-1.80310.18621410.15912653279499
1.8031-1.85180.19151400.15082672281299
1.8518-1.90620.18681340.15092656279098
1.9062-1.96770.18551420.14972650279299
1.9677-2.0380.18981340.14622705283999
2.038-2.11950.18011430.14062667281099
2.1195-2.21580.15081390.138627172856100
2.2158-2.33250.16171450.13842678282399
2.3325-2.47830.17461460.140126932839100
2.4783-2.66920.16261430.142127362879100
2.6692-2.9370.17531510.149527252876100
2.937-3.36020.15881580.151627232881100
3.3602-4.22630.17181500.12692751290199
4.2263-19.5140.17661230.15982566268988
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.95960.28060.69690.68930.40791.8614-0.01310.0917-0.0113-0.03710.0365-0.0978-0.03350.1465-0.02560.0821-0.00320.01660.08660.00480.093511.7333.543643.1552
21.08040.2880.5370.96550.21530.7207-0.00820.0252-0.0113-0.03750.0310.11880.0486-0.0554-0.01930.082-0.01070.02610.10450.01430.1013-5.293534.226841.5939
32.7988-1.16970.34454.1376-0.15662.52930.0823-0.08290.3910.2370.0430.1207-0.3889-0.1055-0.10940.1675-0.00710.04660.12090.02410.2256-12.494554.171140.9073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 353 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 354 through 437 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 518 )A0

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