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- PDB-9ldf: The structure of TkoKptA/DNA/Appr>P complex-A -

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Basic information

Entry
Database: PDB / ID: 9ldf
TitleThe structure of TkoKptA/DNA/Appr>P complex-A
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • Probable RNA 2'-phosphotransferase
KeywordsTRANSFERASE/DNA / Kpta / complex / DNA / Appr> / P / 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
: / IMIDAZOLE / DNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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/Appr>P complex-A
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)24,8485
Polymers24,0652
Non-polymers7823
Water82946
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)85.285, 85.285, 66.850
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: 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(*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, 49 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-A1EJE / [[(3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2,6-bis(oxidanyl)-2-oxidanylidene-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 621.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N5O16P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Ammonium sulfate 50 mM BIS-TRIS pH 6.5 30% v/v Pentaerythritol ethoxylate (15/4 EO/OH)

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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: 1.82→60.31 Å / Num. obs: 18124 / % possible obs: 92 % / Redundancy: 16.2 % / CC1/2: 0.72 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.033 / Rrim(I) all: 0.13 / Net I/σ(I): 12.6
Reflection shellResolution: 1.82→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 3.209 / Num. unique obs: 906 / CC1/2: 0.156 / Rpim(I) all: 1.388 / Rrim(I) all: 3.516

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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: 1.82→33.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 843 4.68 %
Rwork0.2022 --
obs0.2033 18025 79.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 123 50 46 1655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061657
X-RAY DIFFRACTIONf_angle_d0.9122266
X-RAY DIFFRACTIONf_dihedral_angle_d18.025298
X-RAY DIFFRACTIONf_chiral_restr0.055250
X-RAY DIFFRACTIONf_plane_restr0.012269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.940.587290.3741370X-RAY DIFFRACTION10
1.94-2.090.30511460.27242690X-RAY DIFFRACTION77
2.09-2.30.2761820.26073416X-RAY DIFFRACTION97
2.3-2.630.23221350.22063597X-RAY DIFFRACTION100
2.63-3.310.26611770.20773528X-RAY DIFFRACTION98
3.31-33.130.18611940.17033581X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 6.6692 Å / Origin y: -17.8869 Å / Origin z: 0.7842 Å
111213212223313233
T0.1511 Å20.0251 Å20.008 Å2-0.1846 Å2-0.0268 Å2--0.1302 Å2
L6.0725 °20.434 °2-0.2822 °2-1.9274 °20.2465 °2--2.081 °2
S0.0546 Å °-0.1433 Å °0.0044 Å °0.0117 Å °0.0016 Å °-0.0217 Å °-0.151 Å °0.3416 Å °-0.0427 Å °
Refinement TLS groupSelection details: all

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