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- PDB-4pn0: Structure of S. pombe Pct1 RNA triphosphatase -

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Basic information

Entry
Database: PDB / ID: 4pn0
TitleStructure of S. pombe Pct1 RNA triphosphatase
ComponentsmRNA-capping enzyme subunit beta
KeywordsHYDROLASE / mRNA triphosphatase / polynucleotide 5' triphosphatase / mRNA processing / mRNA capping / dimer
Function / homology
Function and homology information


7-methylguanosine RNA capping / polynucleotide 5' dephosphorylation / mRNA capping enzyme complex / 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
mRNA-capping enzyme subunit beta
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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_assembly / 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_assembly.oligomeric_details / _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

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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


Theoretical massNumber of molelcules
Total (without water)142,3454
Polymers142,3454
Non-polymers00
Water4,252236
1
A: mRNA-capping enzyme subunit beta
B: mRNA-capping enzyme subunit beta


Theoretical massNumber of molelcules
Total (without water)71,1732
Polymers71,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-22 kcal/mol
Surface area26190 Å2
MethodPISA
2
C: mRNA-capping enzyme subunit beta
D: mRNA-capping enzyme subunit beta


Theoretical massNumber of molelcules
Total (without water)71,1732
Polymers71,1732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-20 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.340, 93.660, 123.980
Angle α, β, γ (deg.)90.00, 104.10, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 2.8 M NaCl, 10% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 45261 / % possible obs: 91.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.2 / % possible all: 78.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D8I

1d8i


Resolution: 2.6→21.476 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 2151 5.08 %Random selection
Rwork0.1987 ---
obs0.2011 42358 93.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→21.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8496 0 0 236 8732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028656
X-RAY DIFFRACTIONf_angle_d0.64311691
X-RAY DIFFRACTIONf_dihedral_angle_d12.1783359
X-RAY DIFFRACTIONf_chiral_restr0.0461304
X-RAY DIFFRACTIONf_plane_restr0.0021543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.66050.38891360.31982434X-RAY DIFFRACTION85
2.6605-2.72690.34341270.30362569X-RAY DIFFRACTION91
2.7269-2.80050.30221440.28832632X-RAY DIFFRACTION92
2.8005-2.88270.34191110.26772654X-RAY DIFFRACTION92
2.8827-2.97550.31521510.25852601X-RAY DIFFRACTION92
2.9755-3.08160.35021490.25362652X-RAY DIFFRACTION93
3.0816-3.20460.29551490.24162685X-RAY DIFFRACTION94
3.2046-3.34990.27921350.21982716X-RAY DIFFRACTION94
3.3499-3.52580.23811470.19932686X-RAY DIFFRACTION94
3.5258-3.74560.25231530.18622744X-RAY DIFFRACTION96
3.7456-4.0330.23011360.16712757X-RAY DIFFRACTION96
4.033-4.43570.18911550.15162800X-RAY DIFFRACTION96
4.4357-5.07010.17141440.13052768X-RAY DIFFRACTION96
5.0701-6.36020.19421460.1762754X-RAY DIFFRACTION95
6.3602-21.47630.21081680.18082755X-RAY DIFFRACTION94

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