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- PDB-9ld4: The Apo-form structure of TkoKptA -

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Basic information

Entry
Database: PDB / ID: 9ld4
TitleThe Apo-form structure of TkoKptA
ComponentsProbable RNA 2'-phosphotransferase
KeywordsTRANSFERASE / Apo-protein / Kpta
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: 3.61 Å
AuthorsCao, X.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 Apo-form structure of TkoKptA
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

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Assembly

Deposited unit
A: Probable RNA 2'-phosphotransferase
B: Probable RNA 2'-phosphotransferase
C: Probable RNA 2'-phosphotransferase
D: Probable RNA 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)83,9134
Polymers83,9134
Non-polymers00
Water00
1
A: Probable RNA 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)20,9781
Polymers20,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable RNA 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)20,9781
Polymers20,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable RNA 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)20,9781
Polymers20,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable RNA 2'-phosphotransferase


Theoretical massNumber of molelcules
Total (without water)20,9781
Polymers20,9781
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.780, 234.650, 74.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Probable RNA 2'-phosphotransferase / TkoKptA


Mass: 20978.260 Da / Num. of mol.: 4
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
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: 3.17 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% w/v PEG 6000 100 mM Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.61→36.76 Å / Num. obs: 12679 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.356 / Rpim(I) all: 0.101 / Rrim(I) all: 0.371 / Χ2: 1 / Net I/σ(I): 8.6 / Num. measured all: 165979
Reflection shellResolution: 3.61→3.7 Å / % possible obs: 99.9 % / Redundancy: 13.4 % / Rmerge(I) obs: 1.368 / Num. measured all: 12384 / Num. unique obs: 927 / CC1/2: 0.811 / Rpim(I) all: 0.386 / Rrim(I) all: 1.422 / Χ2: 0.97 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.61→36.76 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 619 4.89 %
Rwork0.2316 --
obs0.2329 12664 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.61→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 0 0 5545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025670
X-RAY DIFFRACTIONf_angle_d0.5557680
X-RAY DIFFRACTIONf_dihedral_angle_d11.6342148
X-RAY DIFFRACTIONf_chiral_restr0.046866
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.61-3.970.32981550.27822954X-RAY DIFFRACTION100
3.97-4.550.27981480.23682962X-RAY DIFFRACTION100
4.55-5.720.24661430.23043028X-RAY DIFFRACTION100
5.73-36.760.22391730.2073101X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.2633 Å / Origin y: -65.1941 Å / Origin z: 3.0234 Å
111213212223313233
T0.5209 Å20.0242 Å2-0.0369 Å2-0.6357 Å20.0004 Å2--0.5939 Å2
L0.6647 °20.0136 °2-0.1127 °2-0.26 °2-0.0259 °2--0.7164 °2
S0.0533 Å °0.0538 Å °-0.1176 Å °0.0426 Å °-0.0452 Å °-0.0402 Å °-0.0346 Å °0.0175 Å °-0.0051 Å °
Refinement TLS groupSelection details: all

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