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- PDB-9kma: Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 9kma
TitleCrystal structure of the CCA-adding enzyme from Arabidopsis thaliana
ComponentsPolynucleotide adenylyltransferase family protein
KeywordsRNA BINDING PROTEIN / CCA-adding enzyme / tRNA processing / protein sorting
Function / homologyPoly A polymerase, head domain / Poly A polymerase head domain / tRNA 3'-terminal CCA addition / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / mitochondrion / RNA binding / Polynucleotide adenylyltransferase family protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.229 Å
AuthorsWang, X. / Li, Y.Y. / Dou, Z.Y. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: J Struct Biol X / Year: 2025
Title: Crystal structure of the CCA-adding enzyme from Arabidopsis thaliana .
Authors: Wang, X. / Li, Y.Y. / Dou, Z.Y. / Wang, J. / Liu, L.
History
DepositionNov 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polynucleotide adenylyltransferase family protein


Theoretical massNumber of molelcules
Total (without water)66,1011
Polymers66,1011
Non-polymers00
Water00
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)61.680, 63.906, 152.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polynucleotide adenylyltransferase family protein / tRNA adenylyltransferase-like protein


Mass: 66100.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g22660, T22J18.17, T22J18_17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q94K06
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10054 / % possible obs: 99.4 % / Redundancy: 4.4 % / CC1/2: 0.758 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.2-3.314.60.9199790.7580.9290.4621.0340.845100
3.31-3.454.60.6359710.8180.9490.3170.7130.91100
3.45-3.64.50.42510000.920.9790.2140.4780.981100
3.6-3.794.50.28510150.9550.9880.1440.3211.137100
3.79-4.034.50.2259740.9740.9940.1130.2531.193100
4.03-4.344.50.1719950.9720.9930.0840.1911.0799.7
4.34-4.784.40.1559950.9680.9920.0760.1730.88399.7
4.78-5.474.30.1410340.9770.9940.0690.1570.92499.6
5.47-6.894.20.10710220.9860.9960.0540.120.83899.6
6.89-5040.07710690.9890.9970.0420.0880.68495.8

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.229→44.38 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 485 5.31 %
Rwork0.2585 --
obs0.2605 9142 89.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.229→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 0 0 4057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084157
X-RAY DIFFRACTIONf_angle_d1.1365623
X-RAY DIFFRACTIONf_dihedral_angle_d5.4833523
X-RAY DIFFRACTIONf_chiral_restr0.086645
X-RAY DIFFRACTIONf_plane_restr0.015719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.229-3.69570.32241210.32274X-RAY DIFFRACTION72
3.6957-4.65540.26321850.2453125X-RAY DIFFRACTION99
4.6554-44.380.30981790.2513258X-RAY DIFFRACTION98

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