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- PDB-7c1z: ATP bound structure of Pseudouridine kinase (PUKI) from Arabidops... -

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Basic information

Entry
Database: PDB / ID: 7c1z
TitleATP 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'-TRIPHOSPHATE / Pseudouridine kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09617035687 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
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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)81,87910
Polymers80,7222
Non-polymers1,1588
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-70 kcal/mol
Surface area27770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.613, 47.917, 91.928
Angle α, β, γ (deg.)90.0, 108.948, 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
11METMETPHEPHEchain 'A' and segid ' 'AA1 - 2031 - 203
12LEULEUASNASNchain 'A' and segid ' 'AA210 - 256210 - 256
13PHEPHEPHEPHEchain 'A' and segid ' 'AA268 - 280268 - 280
14SERSERMETMETchain 'A' and segid ' 'AA290 - 372290 - 372
21METMETPHEPHEchain 'B' and segid 'B000'BB1 - 2031 - 203
22LEULEUASNASNchain 'B' and segid 'B000'BB210 - 256210 - 256
23PHEPHEPHEPHEchain 'B' and segid 'B000'BB268 - 280268 - 280
24SERSERMETMETchain 'B' and segid 'B000'BB290 - 372290 - 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 0.1M tri sodium citrate, 22% PEG3350

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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: 2.09→50 Å / Num. obs: 39242 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.3572730567 Å2 / CC1/2: 0.988 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 1116 / CC1/2: 0.609

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09617035687→30.7152450302 Å / SU ML: 0.243352435661 / Cross valid method: NONE / σ(F): 1.33646597268 / Phase error: 24.428406728
RfactorNum. reflection% reflection
Rfree0.237190106125 1999 5.0967593891 %
Rwork0.185695326493 --
obs0.188296511997 39221 99.4674241079 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.2014354609 Å2
Refinement stepCycle: LAST / Resolution: 2.09617035687→30.7152450302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5288 0 68 109 5465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008398435769225442
X-RAY DIFFRACTIONf_angle_d1.254354948247401
X-RAY DIFFRACTIONf_chiral_restr0.0496701906544898
X-RAY DIFFRACTIONf_plane_restr0.0063859984069925
X-RAY DIFFRACTIONf_dihedral_angle_d14.4122144571987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0962-2.14860.303632272541390.2630133858972605X-RAY DIFFRACTION98.8472622478
2.1486-2.20670.2869057343121420.2542852300232637X-RAY DIFFRACTION99.8204022989
2.2067-2.27160.3020176687861440.2320729609582663X-RAY DIFFRACTION99.8932384342
2.2716-2.34490.292568015641410.236725174242627X-RAY DIFFRACTION99.7837058399
2.3449-2.42860.3030870955921440.2242131628452675X-RAY DIFFRACTION99.9645390071
2.4286-2.52580.24496924551420.204829975122669X-RAY DIFFRACTION99.7162114225
2.5258-2.64070.2537274519751400.190058476522620X-RAY DIFFRACTION99.9275887038
2.6407-2.77990.2611485205351440.1860900006072674X-RAY DIFFRACTION99.8582565556
2.7799-2.95390.2285503803141430.1806118041242663X-RAY DIFFRACTION99.8576512456
2.9539-3.18180.2113245437321440.1784578641932666X-RAY DIFFRACTION99.8933522929
3.1818-3.50150.2457896000721440.1779354278982680X-RAY DIFFRACTION99.7527375486
3.5015-4.00730.2111814386891440.168276087832686X-RAY DIFFRACTION99.823633157
4.0073-5.04510.2082183396181430.1564082262942668X-RAY DIFFRACTION99.1184767278
5.0451-30.7150.2336774559931450.1877881044762689X-RAY DIFFRACTION96.4273562436
Refinement TLS params.Method: refined / Origin x: -14.5279865344 Å / Origin y: -6.5629646467 Å / Origin z: 100.931020794 Å
111213212223313233
T0.258767102729 Å20.0275431771955 Å2-0.0355038241997 Å2-0.259467968609 Å20.0274422451412 Å2--0.363488703954 Å2
L0.480322259325 °2-0.11476482211 °2-0.636705428412 °2-0.29756609891 °20.393447663955 °2--1.59448355715 °2
S-0.0559771145475 Å °-0.027971423374 Å °-0.0114127332759 Å °0.061607551473 Å °0.0362761204031 Å °-0.0088951165352 Å °-0.0102607728732 Å °-0.00250135452059 Å °0.0118307084215 Å °
Refinement TLS groupSelection details: all

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