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- PDB-6ede: tRNA 2'-phosphotransferase -

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Basic information

Entry
Database: PDB / ID: 6ede
TitletRNA 2'-phosphotransferase
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / KptA / Tpt1 / TRPT1
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+-protein poly-ADP-ribosyltransferase activity
Similarity search - Function
RNA 2'-phosphotransferase, Tpt1/KptA family, N-terminal domain / 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 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-HQG / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å
AuthorsShuman, S. / Goldgur, Y. / Banerjee, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35 GM126945 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structure of tRNA splicing enzyme Tpt1 illuminates the mechanism of RNA 2'-PO4recognition and ADP-ribosylation.
Authors: Banerjee, A. / Munir, A. / Abdullahu, L. / Damha, M.J. / Goldgur, Y. / Shuman, S.
History
DepositionAug 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,0752
Polymers23,4361
Non-polymers6391
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.284, 53.284, 308.393
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1192-

HOH

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 23435.961 Da / Num. of mol.: 1 / Mutation: C46S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: kptA, Cthe_3059
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A3DJX6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-HQG / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 639.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N5O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.0, 10 %MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 39099 / % possible obs: 99.3 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rpim(I) all: 0.014 / Net I/σ(I): 56.6
Reflection shellResolution: 1.55→1.59 Å / Mean I/σ(I) obs: 2.8 / CC1/2: 0.884 / Rpim(I) all: 0.208 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E3A

6e3a


Resolution: 1.553→46.145 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63
RfactorNum. reflection% reflection
Rfree0.1876 2000 5.14 %
Rwork0.1727 --
obs0.1735 38941 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.553→46.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1459 0 40 201 1700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051537
X-RAY DIFFRACTIONf_angle_d0.8532082
X-RAY DIFFRACTIONf_dihedral_angle_d6.826921
X-RAY DIFFRACTIONf_chiral_restr0.051222
X-RAY DIFFRACTIONf_plane_restr0.005254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5534-1.59220.22861360.2282496X-RAY DIFFRACTION97
1.5922-1.63530.21161370.19772548X-RAY DIFFRACTION100
1.6353-1.68340.22411410.18382584X-RAY DIFFRACTION100
1.6834-1.73770.18521390.17432569X-RAY DIFFRACTION100
1.7377-1.79980.20861390.17562588X-RAY DIFFRACTION100
1.7998-1.87190.17661400.16482585X-RAY DIFFRACTION100
1.8719-1.95710.19391420.16732619X-RAY DIFFRACTION100
1.9571-2.06030.19111410.16842612X-RAY DIFFRACTION100
2.0603-2.18940.2011430.16342617X-RAY DIFFRACTION100
2.1894-2.35840.21931410.17452625X-RAY DIFFRACTION100
2.3584-2.59570.18171440.17912669X-RAY DIFFRACTION100
2.5957-2.97130.17461480.17332716X-RAY DIFFRACTION100
2.9713-3.74320.16081470.15992722X-RAY DIFFRACTION100
3.7432-46.16560.19591620.17742991X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.1205 Å / Origin y: -5.2842 Å / Origin z: 12.6288 Å
111213212223313233
T0.1526 Å20.0147 Å2-0.0038 Å2-0.1294 Å20.0327 Å2--0.1254 Å2
L0.7996 °2-0.7048 °20.0003 °2-2.434 °20.2863 °2--1.3936 °2
S0.0178 Å °0.0041 Å °0.0323 Å °-0.0833 Å °0.0034 Å °0.0215 Å °-0.0664 Å °-0.0127 Å °-0.003 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 4 through 900)

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