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- PDB-4xq0: Structure of fission yeast RNA polymerase II CTD phosphatase Fcp1... -

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Basic information

Entry
Database: PDB / ID: 4xq0
TitleStructure of fission yeast RNA polymerase II CTD phosphatase Fcp1-R271A bound to beryllium fluoride
ComponentsRNA polymerase II subunit A C-terminal domain phosphatase
KeywordsHYDROLASE / Phosphatase / PolII-CTD / Transition state
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 / regulation of transcription by RNA polymerase II / 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
RNA polymerase II subunit A C-terminal domain phosphatase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)43,3587
Polymers42,3621
Non-polymers9956
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-12 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.422, 80.255, 89.196
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 RNA polymerase II subunit A C-terminal domain phosphatase / / CTD phosphatase fcp1


Mass: 42362.316 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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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.: 217 / 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: 47.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 40% PEG-400 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: 1.85→37 Å / Num. obs: 34556 / % possible obs: 99.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.4
Reflection shellResolution: 1.85→1.91 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EF0

3ef0


Resolution: 1.85→36.6 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1654 5.03 %Random selection
Rwork0.158 ---
obs0.16 32886 94.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 48 217 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013043
X-RAY DIFFRACTIONf_angle_d1.0864105
X-RAY DIFFRACTIONf_dihedral_angle_d12.9181165
X-RAY DIFFRACTIONf_chiral_restr0.046459
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90450.25971150.23612377X-RAY DIFFRACTION88
1.9045-1.96590.27351030.21272451X-RAY DIFFRACTION90
1.9659-2.03620.27471410.19072502X-RAY DIFFRACTION93
2.0362-2.11770.2231540.17162536X-RAY DIFFRACTION94
2.1177-2.21410.19851560.15592561X-RAY DIFFRACTION95
2.2141-2.33080.21061390.14512581X-RAY DIFFRACTION95
2.3308-2.47680.16311220.14172611X-RAY DIFFRACTION96
2.4768-2.6680.20841380.14992639X-RAY DIFFRACTION97
2.668-2.93630.1861470.15832666X-RAY DIFFRACTION97
2.9363-3.3610.21921640.16042704X-RAY DIFFRACTION98
3.361-4.23350.18571350.13582771X-RAY DIFFRACTION99
4.2335-36.60190.17191400.15672833X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44691.057-1.43781.864-1.18082.3506-0.02030.11630.10550.04690.11020.1513-0.089-0.218-0.0820.11310.0233-0.02080.1414-0.00880.148715.8478.922348.8335
25.33761.9762-2.94364.069-2.89933.52230.1218-0.04810.25970.1803-0.0233-0.0201-0.2840.2159-0.03310.08520.0380.0030.0845-0.01140.087722.483714.551441.3885
32.08790.0514-0.87660.70070.29793.22520.01590.07180.0136-0.13640.03020.0994-0.0421-0.1222-0.04960.1657-0.0124-0.01220.13860.00760.153418.96327.464736.7669
44.17411.28322.37131.65891.58746.3997-0.13120.60740.0124-0.44550.00140.18710.2948-0.08920.06170.4111-0.0248-0.01420.29860.02120.3258.2559-6.256445.3681
52.54212.546-2.57086.8085-4.80538.2281-0.0426-0.4599-0.33570.214-0.436-0.52650.18630.78570.41170.18290.07120.01070.25570.01610.149821.3612-4.70664.6227
64.97912.7013-4.12086.7669-5.64255.7508-0.0419-0.1170.0589-0.0387-0.2944-0.466-0.16930.57340.28780.1486-0.0521-0.01660.1502-0.02830.182236.40915.665635.366
71.855-2.00791.59668.591-2.78871.60520.04130.30110.032-0.4985-0.1357-0.48380.20.21060.19380.14560.00250.06810.2229-0.01840.209238.85544.012729.2959
84.1561-1.7307-0.06055.2328-0.13413.45980.0499-0.1866-0.45160.36150.13-0.31280.46540.1312-0.1330.24550.0069-0.06240.1893-0.02780.279540.1504-14.040641.0277
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 150 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 246 )
3X-RAY DIFFRACTION3chain 'A' and (resid 247 through 316 )
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 353 )
5X-RAY DIFFRACTION5chain 'A' and (resid 354 through 382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 383 through 408 )
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 437 )
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 518 )

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