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- PDB-9ldg: The structure of TkoKptA/DNA/Appr>P complex-B -

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Basic information

Entry
Database: PDB / ID: 9ldg
TitleThe structure of TkoKptA/DNA/Appr>P complex-B
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
: / DNA / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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-B
Authors: Cao, C.L. / Yang, J. / Zhang, W.Z. / Gan, J.H.
History
DepositionJan 6, 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: Probable RNA 2'-phosphotransferase
C: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
D: DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5578
Polymers48,1314
Non-polymers1,4274
Water70339
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)60.078, 59.397, 65.749
Angle α, β, γ (deg.)90.00, 94.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 20978.260 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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.: 2 / Source method: obtained synthetically / Formula: C15H22N5O16P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM Calcium acetate 20% w/v PEG 3350 pH 7.5

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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 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.26→65.59 Å / Num. obs: 18988 / % possible obs: 86.7 % / Redundancy: 2.4 % / CC1/2: 0.98 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.082 / Rrim(I) all: 0.142 / Net I/σ(I): 4.8
Reflection shellResolution: 2.26→2.38 Å / Rmerge(I) obs: 0.861 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1718 / CC1/2: 0.415 / Rpim(I) all: 0.762 / Rrim(I) all: 1.154

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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: 2.4→29.66 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 840 5 %
Rwork0.2359 --
obs0.2386 16794 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2730 414 90 39 3273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043354
X-RAY DIFFRACTIONf_angle_d0.6634646
X-RAY DIFFRACTIONf_dihedral_angle_d20.732659
X-RAY DIFFRACTIONf_chiral_restr0.045526
X-RAY DIFFRACTIONf_plane_restr0.005520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.550.3651170.34132202X-RAY DIFFRACTION77
2.55-2.750.3961610.30642619X-RAY DIFFRACTION92
2.75-3.020.37471300.28642727X-RAY DIFFRACTION94
3.02-3.460.26921280.23652800X-RAY DIFFRACTION97
3.46-4.360.27221610.20912784X-RAY DIFFRACTION97
4.36-29.660.24771430.20532822X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.82190.69430.87811.49210.27462.8935-0.00250.05270.1814-0.2168-0.13010.1469-0.4833-0.330.13130.72590.09050.03990.2648-0.0450.3137-5.6607-61.1953-31.435
23.0543-0.3716-1.20620.8381-0.10912.8343-0.09220.0347-0.20410.0971-0.04250.1670.1968-0.25730.14160.6538-0.08620.01310.2406-0.04340.3271-8.0703-102.5502-2.4549
32.66751.887-1.60255.116-2.75831.6282-0.0589-0.6761-0.5584-0.10221.03631.53191.7421-1.4055-1.081.7519-0.383-0.1530.94030.36870.7595-15.9744-80.499-21.1516
44.56083.5952-3.72689.5468-7.23465.80430.1841.07660.8752-0.29140.95391.8699-1.3981-0.9068-1.47841.398-0.0995-0.14340.92280.21920.6959-16.9021-83.4463-14.4444
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 4:180)
2X-RAY DIFFRACTION2(chain B and resseq 5:180)
3X-RAY DIFFRACTION3(chain C and resseq 1:10)
4X-RAY DIFFRACTION4(chain D and resseq 1:10)

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