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- PDB-9ldh: The complex structure of TkoKptA/2',3',5'-p-U -

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Basic information

Entry
Database: PDB / ID: 9ldh
TitleThe complex structure of TkoKptA/2',3',5'-p-U
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / Kpta / complex / 2' / 3' / 5'-p-U
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
: / Probable RNA 2'-phosphotransferase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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/2',3',5'-p-U
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

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0398
Polymers20,9781
Non-polymers1,0617
Water32418
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)58.450, 58.450, 222.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1EJD / [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-diphosphonooxy-oxolan-2-yl]methyl dihydrogen phosphate / 3h-Uridine tri-phosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 200 mM Ammonium sulfate 20% w/v PEG 3350 pH 6.0

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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: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→29.23 Å / Num. obs: 17731 / % possible obs: 99.8 % / Redundancy: 30.2 % / CC1/2: 1 / CC star: 0.011 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.06 / Net I/σ(I): 33
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 19.6 % / Rmerge(I) obs: 1.273 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1233 / CC1/2: 0.812 / Rpim(I) all: 0.292 / Rrim(I) all: 1.308

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→25.15 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 860 4.88 %
Rwork0.2183 --
obs0.2206 17632 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→25.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 0 59 18 1525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011531
X-RAY DIFFRACTIONf_angle_d1.1992076
X-RAY DIFFRACTIONf_dihedral_angle_d6.786224
X-RAY DIFFRACTIONf_chiral_restr0.072223
X-RAY DIFFRACTIONf_plane_restr0.017265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.060.29621310.2522683X-RAY DIFFRACTION99
2.06-2.220.30791280.24742725X-RAY DIFFRACTION100
2.22-2.440.29041520.25212750X-RAY DIFFRACTION100
2.44-2.80.30851370.25172769X-RAY DIFFRACTION100
2.8-3.520.29341620.24082805X-RAY DIFFRACTION100
3.52-25.150.23091500.19193040X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.4812 Å / Origin y: -13.9113 Å / Origin z: 2.8241 Å
111213212223313233
T0.3532 Å20.0229 Å20.0497 Å2-0.2672 Å20.0661 Å2--0.3056 Å2
L3.8563 °21.9954 °22.9744 °2-3.2678 °21.8407 °2--3.6103 °2
S-0.1036 Å °-0.1403 Å °0.1026 Å °0.0824 Å °-0.0276 Å °0.1509 Å °-0.0319 Å °-0.1436 Å °0.1223 Å °
Refinement TLS groupSelection details: all

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