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- PDB-9ld6: The complex structure of TkoKptA/DNA/NAD+ -

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Basic information

Entry
Database: PDB / ID: 9ld6
TitleThe complex structure of TkoKptA/DNA/NAD+
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Probable RNA 2'-phosphotransferase
KeywordsTRANSFERASE/DNA / Kpta / complex / DNA / NAD+ / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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 complex structure of TkoKptA/DNA/NAD+
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
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0136
Polymers24,0652
Non-polymers9484
Water1086
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)83.637, 83.637, 67.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 20978.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: 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(*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)

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Non-polymers , 4 types, 10 molecules

#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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 200 mM Sodium chloride 20% w/v PEG 3350 pH 6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.01→59.14 Å / Num. obs: 16517 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.039 / Rrim(I) all: 0.177 / Χ2: 0.66 / Net I/σ(I): 11.5 / Num. measured all: 341575
Reflection shellResolution: 2.01→2.12 Å / % possible obs: 100 % / Redundancy: 16.4 % / Rmerge(I) obs: 6.207 / Num. measured all: 38833 / Num. unique obs: 2372 / CC1/2: 0.482 / Rpim(I) all: 1.549 / Rrim(I) all: 6.402 / Χ2: 0.3 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→32.75 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 772 5.03 %
Rwork0.2344 --
obs0.2366 15334 93.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→32.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 57 60 6 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081554
X-RAY DIFFRACTIONf_angle_d1.0372122
X-RAY DIFFRACTIONf_dihedral_angle_d13.529261
X-RAY DIFFRACTIONf_chiral_restr0.062238
X-RAY DIFFRACTIONf_plane_restr0.01258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.140.36281100.34221741X-RAY DIFFRACTION69
2.14-2.310.3681080.39282378X-RAY DIFFRACTION93
2.31-2.540.38921250.33952501X-RAY DIFFRACTION97
2.54-2.90.35721330.29882581X-RAY DIFFRACTION100
2.9-3.660.28431520.23092594X-RAY DIFFRACTION100
3.66-32.750.22731440.18672767X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.3797 Å / Origin y: -18.0371 Å / Origin z: 1.6535 Å
111213212223313233
T0.2416 Å20.0487 Å20.0318 Å2-0.4539 Å2-0.0057 Å2--0.2257 Å2
L6.9694 °20.1531 °2-0.1701 °2-2.0377 °20.3927 °2--1.8973 °2
S0.0046 Å °-0.1997 Å °-0.1162 Å °0.0111 Å °0.0131 Å °-0.0525 Å °-0.043 Å °0.6391 Å °-0.0354 Å °
Refinement TLS groupSelection details: all

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