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- PDB-4pn1: Structure of S. pombe Pct1 RNA triphosphatase in complex with the... -

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Basic information

Entry
Database: PDB / ID: 4pn1
TitleStructure of S. pombe Pct1 RNA triphosphatase in complex with the Spt5 CTD
Components
  • Synthetic peptide
  • mRNA-capping enzyme subunit beta
KeywordsHYDROLASE/TRANSCRIPTION REGULATOR / mRNA triphosphatase / hydrolase / polynucleotide 5' triphosphatase / mRNA processing / mRNA capping / dimer / transcription elongation factor / HYDROLASE-TRANSCRIPTION REGULATOR complex
Function / homology
Function and homology information


mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / RNA polymerase II C-terminal domain binding / 7-methylguanosine mRNA capping / ATP hydrolysis activity / nucleus
Similarity search - Function
mRNA triphosphatase Cet1-like / RNA 5'-triphosphatase Cet1/Ctl1 / mRNA capping enzyme, beta chain / mRNA triphosphatase Cet1-like / mRNA triphosphatase Cet1-like superfamily / mRNA Triphosphatase Cet1; Chain A / CYTH-like domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / mRNA-capping enzyme subunit beta
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsLima, C.D. / Doamekpor, S.K.
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: Fission yeast RNA triphosphatase reads an Spt5 CTD code.
Authors: Doamekpor, S.K. / Schwer, B. / Sanchez, A.M. / Shuman, S. / Lima, C.D.
History
DepositionMay 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 31, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
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_database_status.pdb_format_compatible / _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 / refine_hist
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: mRNA-capping enzyme subunit beta
B: mRNA-capping enzyme subunit beta
C: mRNA-capping enzyme subunit beta
D: mRNA-capping enzyme subunit beta
E: Synthetic peptide
F: Synthetic peptide
G: Synthetic peptide
H: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,37016
Polymers149,9698
Non-polymers4008
Water2,252125
1
A: mRNA-capping enzyme subunit beta
B: mRNA-capping enzyme subunit beta
E: Synthetic peptide
F: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2479
Polymers74,9854
Non-polymers2625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-34 kcal/mol
Surface area26220 Å2
MethodPISA
2
C: mRNA-capping enzyme subunit beta
D: mRNA-capping enzyme subunit beta
G: Synthetic peptide
H: Synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1237
Polymers74,9854
Non-polymers1383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-36 kcal/mol
Surface area25240 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14720 Å2
ΔGint-77 kcal/mol
Surface area49770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.603, 251.542, 75.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
mRNA-capping enzyme subunit beta / Polynucleotide 5'-triphosphatase / mRNA 5'-triphosphatase / TPase


Mass: 35586.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: pct1 / Plasmid: pSMT3 / Details (production host): his-tagged SUMO fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): codon plus RIL / References: UniProt: Q9P6Q6, polynucleotide 5'-phosphatase
#2: Protein/peptide
Synthetic peptide


Mass: 1906.022 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: synthetic peptide derived from the repeating sequence found at the C-terminal domain of Spt5
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 3.0 M sodium formate cryo-protected in 3.2 M sodium formate and 20% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 49568 / % possible obs: 99.1 % / Redundancy: 4.9 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PN0

4pn0


Resolution: 2.803→48.362 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 2236 4.95 %Random selection
Rwork0.1914 ---
obs0.1942 45150 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.2 Å2
Refinement stepCycle: LAST / Resolution: 2.803→48.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8672 0 26 125 8823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038855
X-RAY DIFFRACTIONf_angle_d0.68111946
X-RAY DIFFRACTIONf_dihedral_angle_d13.7343412
X-RAY DIFFRACTIONf_chiral_restr0.0511327
X-RAY DIFFRACTIONf_plane_restr0.0031573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8033-2.86420.32151250.26022568X-RAY DIFFRACTION97
2.8642-2.93080.34871200.25712676X-RAY DIFFRACTION99
2.9308-3.00410.31761240.24712646X-RAY DIFFRACTION99
3.0041-3.08530.29671310.22812652X-RAY DIFFRACTION99
3.0853-3.17610.3091430.22072638X-RAY DIFFRACTION99
3.1761-3.27860.26621440.19922663X-RAY DIFFRACTION99
3.2786-3.39580.26711490.18912628X-RAY DIFFRACTION99
3.3958-3.53170.27441380.18762674X-RAY DIFFRACTION99
3.5317-3.69240.22881370.18022676X-RAY DIFFRACTION100
3.6924-3.8870.22711540.17092665X-RAY DIFFRACTION100
3.887-4.13040.2311360.16122695X-RAY DIFFRACTION99
4.1304-4.44910.21681460.14862702X-RAY DIFFRACTION99
4.4491-4.89640.19331380.13712696X-RAY DIFFRACTION99
4.8964-5.6040.20991510.16872727X-RAY DIFFRACTION99
5.604-7.0570.26991440.22392762X-RAY DIFFRACTION100
7.057-48.36880.24241560.22982846X-RAY DIFFRACTION98

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