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- PDB-8tg6: tRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in comple... -

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Basic information

Entry
Database: PDB / ID: 8tg6
TitletRNA 2'-phosphotransferase (Tpt1) from Aeropyrum pernix in complex with sulfate anions
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / tRNA 2'-PHOSPHOTRANSFERASE / TPT1 / tRNA SPLICING / sulphate ions / Aeropyrum pernix
Function / homology
Function and homology information


tRNA 2'-phosphotransferase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / tRNA splicing, via endonucleolytic cleavage and ligation / NAD+ poly-ADP-ribosyltransferase activity
Similarity search - Function
RNA 2'-phosphotransferase KptA, putative / Phosphotransferase KptA/Tpt1 / RNA 2'-phosphotransferase, N-terminal domain / RNA 2'-phosphotransferase, C-terminal domain / RNA 2'-phosphotransferase, Tpt1 / KptA family
Similarity search - Domain/homology
Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJacewicz, A. / Dantuluri, S. / Shuman, S.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-GM124165 United States
Other governmentHEI-S10OD021527 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structural basis for Tpt1-catalyzed 2'-PO 4 transfer from RNA and NADP(H) to NAD.
Authors: Jacewicz, A. / Dantuluri, S. / Shuman, S.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,29213
Polymers23,3821
Non-polymers91012
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.679, 101.679, 101.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-208-

SO4

21A-440-

HOH

31A-447-

HOH

41A-448-

HOH

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 23382.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: kptA, APE_0204.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon Plus
References: UniProt: Q9YFP5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES-Na, pH 7.5, 1.0 M ammonium sulfate, 2% PEG-400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→66.41 Å / Num. obs: 26676 / % possible obs: 100 % / Redundancy: 17 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.016 / Net I/σ(I): 31.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 17 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1302 / CC1/2: 0.952 / Rpim(I) all: 0.156 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wfx

1wfx


Resolution: 1.6→66.41 Å / SU ML: 0.1483 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1818 1349 5.06 %
Rwork0.1428 25326 -
obs0.1449 26675 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.27 Å2
Refinement stepCycle: LAST / Resolution: 1.6→66.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 44 148 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171549
X-RAY DIFFRACTIONf_angle_d1.29882106
X-RAY DIFFRACTIONf_chiral_restr0.0815225
X-RAY DIFFRACTIONf_plane_restr0.019265
X-RAY DIFFRACTIONf_dihedral_angle_d6.7367217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.660.23111300.15992509X-RAY DIFFRACTION99.89
1.66-1.720.21241390.13062502X-RAY DIFFRACTION100
1.72-1.80.18071420.11272499X-RAY DIFFRACTION100
1.8-1.90.16871480.1172492X-RAY DIFFRACTION100
1.9-2.020.18021190.12962530X-RAY DIFFRACTION100
2.02-2.170.17641230.11822549X-RAY DIFFRACTION100
2.17-2.390.16521290.13472524X-RAY DIFFRACTION100
2.39-2.730.22651270.15262548X-RAY DIFFRACTION99.96
2.74-3.440.17741320.16052555X-RAY DIFFRACTION99.93
3.45-66.410.17061600.14942618X-RAY DIFFRACTION99.75

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