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- PDB-9lde: The complex structure of K63A/2'-p-ADPR-RNA -

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Basic information

Entry
Database: PDB / ID: 9lde
TitleThe complex structure of K63A/2'-p-ADPR-RNA
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / Kpta / complex / mutat / 2'-p-ADPR-RNA
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
ADENOSINE-3'-5'-DIPHOSPHATE / Chem-HQG / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
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 complex structure of K63A/2'-p-ADPR-RNA
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: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2509
Polymers41,8402
Non-polymers2,4097
Water2,054114
1
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2636
Polymers20,9201
Non-polymers1,3435
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9873
Polymers20,9201
Non-polymers1,0662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.253, 89.708, 66.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable RNA 2'-phosphotransferase


Mass: 20920.156 Da / Num. of mol.: 2 / Mutation: K63A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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.: 2 / Source method: obtained synthetically / Formula: C15H24N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 40 mM Citric acid 60 mM BIS-TRIS propane pH 6.4 20% w/v PEG 3350

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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: 1.97→66.19 Å / Num. obs: 25041 / % possible obs: 82.1 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Χ2: 0.82 / Net I/σ(I): 10 / Num. measured all: 148224
Reflection shellResolution: 1.97→2.08 Å / % possible obs: 36.6 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.521 / Num. measured all: 2302 / Num. unique obs: 1563 / CC1/2: 0.659 / Rpim(I) all: 0.472 / Rrim(I) all: 0.706 / Χ2: 0.37 / Net I/σ(I) obs: 2

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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: 1.97→55.79 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 1213 4.87 %
Rwork0.1785 --
obs0.1806 24896 81.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→55.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 150 114 3088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053039
X-RAY DIFFRACTIONf_angle_d0.9494133
X-RAY DIFFRACTIONf_dihedral_angle_d10.014523
X-RAY DIFFRACTIONf_chiral_restr0.054461
X-RAY DIFFRACTIONf_plane_restr0.011529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.050.2593380.2523957X-RAY DIFFRACTION30
2.05-2.150.2517790.20741578X-RAY DIFFRACTION50
2.15-2.260.2584900.20242179X-RAY DIFFRACTION68
2.26-2.40.26681720.20442713X-RAY DIFFRACTION86
2.4-2.590.25911620.20153142X-RAY DIFFRACTION98
2.59-2.850.25271750.19883199X-RAY DIFFRACTION100
2.85-3.260.23091490.18963260X-RAY DIFFRACTION100
3.26-4.10.20081860.15433245X-RAY DIFFRACTION100
4.1-55.790.17871620.15313410X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.4431 Å / Origin y: 23.4346 Å / Origin z: 43.8854 Å
111213212223313233
T0.0923 Å20.0031 Å20.0018 Å2-0.0807 Å20.0159 Å2--0.111 Å2
L0.3261 °2-0.11 °2-0.1705 °2-0.4598 °20.4745 °2--0.8682 °2
S-0.0137 Å °0.0003 Å °-0.0172 Å °0.0232 Å °-0.0165 Å °0.0148 Å °0.0469 Å °0.0204 Å °0.0307 Å °
Refinement TLS groupSelection details: all

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