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- PDB-9ld3: The complex structure of K63A/2',3',5'-P-A/ADPR -

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Basic information

Entry
Database: PDB / ID: 9ld3
TitleThe complex structure of K63A/2',3',5'-P-A/ADPR
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / Kpta / complex / mutat / 2' / 3' / 5'-p-A / ADPR
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
: / Chem-AR6 / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
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 complex structure of K63A/2',3',5'-P-A/ADPR
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)44,1578
Polymers41,8402
Non-polymers2,3176
Water4,396244
1
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0794
Polymers20,9201
Non-polymers1,1593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0794
Polymers20,9201
Non-polymers1,1593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.647, 87.862, 65.528
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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1EJC / [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-diphosphonooxy-oxolan-2-yl]methyl dihydrogen phosphate / Adenosine trisphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 100mM Calcium acetate 100mM imidazole pH 8.0 10% w/v PEG 8000

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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: 1.82→71.65 Å / Num. obs: 37306 / % possible obs: 98.7 % / Redundancy: 10 % / CC1/2: 0.991 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.048 / Rrim(I) all: 0.151 / Χ2: 0.8 / Net I/σ(I): 10.9 / Num. measured all: 371733
Reflection shellResolution: 1.82→1.87 Å / % possible obs: 89.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 1.208 / Num. measured all: 10474 / Num. unique obs: 2433 / CC1/2: 0.34 / Rpim(I) all: 0.661 / Rrim(I) all: 1.393 / Χ2: 0.57 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→55.53 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1793 4.82 %
Rwork0.1782 --
obs0.1801 37224 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→55.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 146 244 3261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083090
X-RAY DIFFRACTIONf_angle_d1.0824201
X-RAY DIFFRACTIONf_dihedral_angle_d10.614597
X-RAY DIFFRACTIONf_chiral_restr0.067467
X-RAY DIFFRACTIONf_plane_restr0.011533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.30571370.25272399X-RAY DIFFRACTION88
1.87-1.920.25291270.21742587X-RAY DIFFRACTION95
1.92-1.990.23581460.19522659X-RAY DIFFRACTION98
1.99-2.060.2581300.1942717X-RAY DIFFRACTION100
2.06-2.140.23221370.18852749X-RAY DIFFRACTION100
2.14-2.240.25961320.17982735X-RAY DIFFRACTION100
2.24-2.360.26311360.18692739X-RAY DIFFRACTION100
2.36-2.50.22481360.17882761X-RAY DIFFRACTION100
2.5-2.70.24071360.19312765X-RAY DIFFRACTION100
2.7-2.970.23221270.18642792X-RAY DIFFRACTION100
2.97-3.40.19851540.17482770X-RAY DIFFRACTION100
3.4-4.280.19081320.14822835X-RAY DIFFRACTION100
4.28-55.530.15981630.16142923X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.6879 Å / Origin y: 23.1036 Å / Origin z: 43.6365 Å
111213212223313233
T0.0806 Å20.001 Å2-0.0005 Å2-0.0732 Å20.0186 Å2--0.0986 Å2
L0.3083 °2-0.0844 °2-0.1881 °2-0.3719 °20.3637 °2--0.6819 °2
S-0.019 Å °-0.0123 Å °-0.035 Å °0.0135 Å °-0.0205 Å °0.0244 Å °0.0288 Å °0.0195 Å °0.03 Å °
Refinement TLS groupSelection details: all

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