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- PDB-7c1x: Unliganded structure of Pseudouridine kinase (PUKI) from Arabidop... -

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Basic information

Entry
Database: PDB / ID: 7c1x
TitleUnliganded 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 / 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
Pseudouridine kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38942849211 Å
AuthorsKim, S.H. / Rhee, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A4A1018890 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
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ncs_dom_lim.selection_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)81,7064
Polymers81,6602
Non-polymers462
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-34 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.686, 48.352, 92.751
Angle α, β, γ (deg.)90.0, 109.144, 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:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPHEPHEchain 'A' and segid ' 'AA2 - 542 - 54
12ILEILESERSERchain 'A' and segid ' 'AA56 - 7556 - 75
13LYSLYSLEULEUchain 'A' and segid ' 'AA77 - 13277 - 132
14VALVALILEILEchain 'A' and segid ' 'AA134 - 188134 - 188
15ALAALAHISHISchain 'A' and segid ' 'AA191 - 201191 - 201
16LEULEUASPASPchain 'A' and segid ' 'AA210 - 214210 - 214
17PHEPHELEULEUchain 'A' and segid ' 'AA216 - 255216 - 255
18VALVALPHEPHEchain 'A' and segid ' 'AA267 - 280267 - 280
19SERSERPHEPHEchain 'A' and segid ' 'AA290 - 292290 - 292
110HISHISALAALAchain 'A' and segid ' 'AA295 - 368295 - 368
111LEULEULEULEUchain 'A' and segid ' 'AA371371
21GLUGLUPHEPHEchain 'B' and segid 'B000'BB2 - 542 - 54
22ILEILESERSERchain 'B' and segid 'B000'BB56 - 7556 - 75
23LYSLYSLEULEUchain 'B' and segid 'B000'BB77 - 13277 - 132
24VALVALILEILEchain 'B' and segid 'B000'BB134 - 188134 - 188
25ALAALAHISHISchain 'B' and segid 'B000'BB191 - 201191 - 201
26LEULEUASPASPchain 'B' and segid 'B000'BB210 - 214210 - 214
27PHEPHELEULEUchain 'B' and segid 'B000'BB216 - 255216 - 255
28VALVALPHEPHEchain 'B' and segid 'B000'BB267 - 280267 - 280
29SERSERPHEPHEchain 'B' and segid 'B000'BB290 - 292290 - 292
210HISHISALAALAchain 'B' and segid 'B000'BB295 - 368295 - 368
211LEULEULEULEUchain 'B' and segid 'B000'BB371371

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Components

#1: Protein PfkB-like carbohydrate kinase family protein


Mass: 40829.836 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / 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: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 26768 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 48.3132469646 Å2 / CC1/2: 0.973 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 781 / CC1/2: 0.728

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.38942849211→29.9316609607 Å / SU ML: 0.307412280363 / Cross valid method: NONE / σ(F): 1.33784333506 / Phase error: 27.132790229
RfactorNum. reflection% reflection
Rfree0.24224659882 1999 7.48548960869 %
Rwork0.208256497175 24706 -
obs0.210811925093 26705 98.1512790356 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.799507558 Å2
Refinement stepCycle: LAST / Resolution: 2.38942849211→29.9316609607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 2 27 5225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003454268444335279
X-RAY DIFFRACTIONf_angle_d0.8931453755487172
X-RAY DIFFRACTIONf_chiral_restr0.0298720644954885
X-RAY DIFFRACTIONf_plane_restr0.00395203904899905
X-RAY DIFFRACTIONf_dihedral_angle_d13.40621521671906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3895-2.44920.3694845143551250.3034537056641540X-RAY DIFFRACTION86.2694300518
2.4492-2.51530.2987755086531410.2713230864471757X-RAY DIFFRACTION98.9056800417
2.5153-2.58930.3270413588311420.2676976682361751X-RAY DIFFRACTION99.0062761506
2.5893-2.67280.3029810679421470.2501040038071811X-RAY DIFFRACTION99.1392405063
2.6728-2.76830.2499671142241390.2301687875521728X-RAY DIFFRACTION98.9925768823
2.7683-2.87910.2630577534581430.2351713768871758X-RAY DIFFRACTION98.650752465
2.8791-3.010.2812891517691430.2366598725431783X-RAY DIFFRACTION99.0231362468
3.01-3.16850.2578785887131420.219770989971754X-RAY DIFFRACTION99.4753410283
3.1685-3.36680.263362684671470.2273466074961815X-RAY DIFFRACTION99.8981670061
3.3668-3.62630.2653380529091440.2201310153441785X-RAY DIFFRACTION99.6384297521
3.6263-3.99050.2506545076191420.2035201903021743X-RAY DIFFRACTION97.4160206718
3.9905-4.56620.1885968995511460.1730183750641799X-RAY DIFFRACTION99.5903737839
4.5662-5.74620.236513561111480.18985252971825X-RAY DIFFRACTION99.4957135653
5.7462-29.930.2053705008621500.1873226790781857X-RAY DIFFRACTION98.6240786241
Refinement TLS params.Method: refined / Origin x: 65.4668434821 Å / Origin y: -15.9664275192 Å / Origin z: 102.071113972 Å
111213212223313233
T0.275556344829 Å20.0519591258227 Å2-0.0664428096163 Å2-0.355595249718 Å20.0327321668863 Å2--0.515135422111 Å2
L0.443628134269 °20.00500897674435 °2-0.450111427511 °2-0.294700096919 °20.270329745645 °2--1.56068515306 °2
S-0.0814425180387 Å °-0.0430506148779 Å °0.00493050278494 Å °0.0580864177129 Å °0.0278449004998 Å °0.000677346490131 Å °-0.0389034402983 Å °-0.0527351045594 Å °0.0344965040516 Å °
Refinement TLS groupSelection details: all

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