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- PDB-9ldc: The structure of TkoKptA/DNA/ADPR complex-B* -

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Basic information

Entry
Database: PDB / ID: 9ldc
TitleThe structure of TkoKptA/DNA/ADPR complex-B*
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Probable RNA 2'-phosphotransferase
KeywordsTRANSFERASE/DNA / Kpta / complex / DNA / ADPR / TRANSFERASE-DNA complex
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
DNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsCao, C.L. / Yang, J. / Zhang, W.Z. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The structure of TkoKptA/DNA/ADPR complex-B*
Authors: Cao, C.L. / Yang, J. / Zhang, W.Z. / Gan, J.H.
History
DepositionJan 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
B: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8905
Polymers24,6062
Non-polymers2843
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.256, 84.256, 66.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 21518.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: kptA, TK0302 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JFX3, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3087.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10mM Cobalt chloride 100mM MES pH 6.5 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→59.58 Å / Num. obs: 16782 / % possible obs: 96 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.015 / Rrim(I) all: 0.066 / Χ2: 0.87 / Net I/σ(I): 26.1 / Num. measured all: 336247
Reflection shellResolution: 1.97→2.08 Å / % possible obs: 100 % / Redundancy: 21.1 % / Rmerge(I) obs: 1.054 / Num. measured all: 52496 / Num. unique obs: 2492 / CC1/2: 0.872 / Rpim(I) all: 0.234 / Rrim(I) all: 1.08 / Χ2: 0.72 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→27.19 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 787 4.7 %
Rwork0.2009 --
obs0.2056 16733 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→27.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 63 51 66 1612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151625
X-RAY DIFFRACTIONf_angle_d1.4632211
X-RAY DIFFRACTIONf_dihedral_angle_d20.617646
X-RAY DIFFRACTIONf_chiral_restr0.08239
X-RAY DIFFRACTIONf_plane_restr0.02268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.10.2761150.20122724X-RAY DIFFRACTION100
2.1-2.260.25591170.20082245X-RAY DIFFRACTION83
2.26-2.480.23791180.21852759X-RAY DIFFRACTION100
2.49-2.840.26061560.22492723X-RAY DIFFRACTION100
2.85-3.580.24861460.21022776X-RAY DIFFRACTION100
3.58-27.190.21591350.18252719X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -6.3797 Å / Origin y: 18.1739 Å / Origin z: 0.691 Å
111213212223313233
T0.3389 Å20.0176 Å2-0.0232 Å2-0.3742 Å20.0264 Å2--0.3099 Å2
L4.2266 °20.68 °20.1526 °2-0.6022 °2-0.2453 °2--0.8787 °2
S0.0963 Å °0.0168 Å °0.0187 Å °-0.0139 Å °-0.0062 Å °-0.0605 Å °0.0336 Å °-0.1597 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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