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- PDB-7c1y: Pseudouridine and ADP bound structure of Pseudouridine kinase (PU... -

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Basic information

Entry
Database: PDB / ID: 7c1y
TitlePseudouridine and ADP bound structure of Pseudouridine kinase (PUKI) from Arabidopsis thaliana
ComponentsPfkB-like carbohydrate kinase family protein
KeywordsRNA / Pseudouridine / kinase / psedouridine kinase / PUKI
Function / homology
Function and homology information


pseudouridine kinase / peroxisome / kinase activity / phosphorylation / ATP binding / metal ion binding
Similarity search - Function
Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 1. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-FJF / Pseudouridine kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.0834261145 Å
AuthorsKim, S.H. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01325801 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana.
Authors: Kim, S.H. / Witte, C.P. / Rhee, S.
History
DepositionMay 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfkB-like carbohydrate kinase family protein
B: PfkB-like carbohydrate kinase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1118
Polymers80,7222
Non-polymers1,3896
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.328, 48.857, 91.788
Angle α, β, γ (deg.)90.0, 107.515, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and segid ' 'A1 - 203
121chain 'A' and segid ' 'A210 - 255
131chain 'A' and segid ' 'A270 - 277
141chain 'A' and segid ' 'A290 - 372
211chain 'B' and segid 'B000'B1 - 203
221chain 'B' and segid 'B000'B210 - 255
231chain 'B' and segid 'B000'B270 - 277
241chain 'B' and segid 'B000'B290 - 372

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Components

#1: Protein PfkB-like carbohydrate kinase family protein


Mass: 40360.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g49350, F13F21.22, F13F21_22 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q94AT3
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FJF / 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione / Pseudouridine


Mass: 244.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.1M tri sodium citrate, 22%PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 39942 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 43.1404012689 Å2 / CC1/2: 0.984 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1069 / CC1/2: 0.524

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.0834261145→30.6196596486 Å / SU ML: 0.294057737643 / Cross valid method: NONE / σ(F): 1.33647786203 / Phase error: 27.5267897635
RfactorNum. reflection% reflection
Rfree0.235049518704 2000 5.01190327027 %
Rwork0.19047965698 37905 -
obs0.192776411402 39905 98.4749401574 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.6595262309 Å2
Refinement stepCycle: LAST / Resolution: 2.0834261145→30.6196596486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 90 83 5380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008307969942955388
X-RAY DIFFRACTIONf_angle_d1.234196144347329
X-RAY DIFFRACTIONf_chiral_restr0.0494882358451898
X-RAY DIFFRACTIONf_plane_restr0.00545791083753912
X-RAY DIFFRACTIONf_dihedral_angle_d13.98501553161949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13550.3726660737121230.3105017465842331X-RAY DIFFRACTION84.9134948097
2.1355-2.19320.3236394112751410.2766338730422686X-RAY DIFFRACTION99.9293036409
2.1932-2.25780.3114786206491450.2557996981352743X-RAY DIFFRACTION99.9307958478
2.2578-2.33060.3269263775761440.2407144124412720X-RAY DIFFRACTION99.965095986
2.3306-2.41390.2817538770161440.2374822086422718X-RAY DIFFRACTION99.8604326588
2.4139-2.51050.29211626961440.2258798267782738X-RAY DIFFRACTION99.9653139091
2.5105-2.62470.2776008344271450.2092752040692735X-RAY DIFFRACTION99.8266897747
2.6247-2.7630.2581974139641430.2108189550242722X-RAY DIFFRACTION99.9302406697
2.763-2.93590.3117663460311440.2078412423212740X-RAY DIFFRACTION99.8960859023
2.9359-3.16240.2645583245131450.2038857158292739X-RAY DIFFRACTION99.7923875433
3.1624-3.48030.2339935153651470.1864677971862772X-RAY DIFFRACTION99.7948717949
3.4803-3.98290.1940730252661440.1729095410812739X-RAY DIFFRACTION99.8614478698
3.9829-5.01450.1880936327221460.1510570985092782X-RAY DIFFRACTION99.5918367347
5.0145-30.610.2141783406851450.1798813749832740X-RAY DIFFRACTION95.5931080186
Refinement TLS params.Method: refined / Origin x: 1.5684859715 Å / Origin y: -7.15134218936 Å / Origin z: 57.345600383 Å
111213212223313233
T0.240152782223 Å20.0361896096652 Å2-0.00627825507392 Å2-0.29135985056 Å20.0618686015936 Å2--0.356111450031 Å2
L0.711683364099 °2-0.0489280633594 °2-0.714402504443 °2-0.91784066782 °20.469484203465 °2--2.26629336633 °2
S-0.0963826808772 Å °-0.0708472923425 Å °-0.0854861587216 Å °0.179547944555 Å °0.00857961704474 Å °0.0369138258746 Å °-0.0246343053824 Å °-0.110147060841 Å °0.0903816113421 Å °
Refinement TLS groupSelection details: all

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