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- PDB-6yk1: Crystal structure of mouse pyridoxal kinase in complex with ATP-g... -

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Basic information

Entry
Database: PDB / ID: 6yk1
TitleCrystal structure of mouse pyridoxal kinase in complex with ATP-gamma-S and artesunate
ComponentsPyridoxal kinase
KeywordsTRANSFERASE / PDXK / PLP / PL / Vitamin B6 / Enzyme / artemisinin / artesunate
Function / homology
Function and homology information


Vitamin B6 activation to pyridoxal phosphate / pyridoxal binding / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / pyridoxal phosphate biosynthetic process / organic cyclic compound binding / sodium ion binding / potassium ion binding ...Vitamin B6 activation to pyridoxal phosphate / pyridoxal binding / lithium ion binding / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / pyridoxal phosphate biosynthetic process / organic cyclic compound binding / sodium ion binding / potassium ion binding / small molecule binding / Neutrophil degranulation / pyridoxal phosphate binding / phosphorylation / negative regulation of apoptotic process / magnesium ion binding / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase-like
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Artesunate / Pyridoxal kinase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKasaragod, V.B. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHI425/8-2 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Pyridoxal kinase inhibition by artemisinins down-regulates inhibitory neurotransmission.
Authors: Kasaragod, V.B. / Pacios-Michelena, A. / Schaefer, N. / Zheng, F. / Bader, N. / Alzheimer, C. / Villmann, C. / Schindelin, H.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal kinase
B: Pyridoxal kinase
C: Pyridoxal kinase
D: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,68742
Polymers140,8494
Non-polymers4,83838
Water2,504139
1
A: Pyridoxal kinase
B: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,31925
Polymers70,4252
Non-polymers2,89523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Pyridoxal kinase
D: Pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,36817
Polymers70,4252
Non-polymers1,94315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)279.380, 53.037, 110.149
Angle α, β, γ (deg.)90.00, 91.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pyridoxal kinase / Pyridoxine kinase


Mass: 35212.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdxk, Pkh / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K183, pyridoxal kinase

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Non-polymers , 6 types, 177 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-D95 / Artesunate


Mass: 384.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.18-0.24 M sodium thiocyanate and 18-26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.4→47.2 Å / Num. obs: 63594 / % possible obs: 0.996 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04648 / Rpim(I) all: 0.053 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.069 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6235 / CC1/2: 0.541 / Rpim(I) all: 0.704 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXT

2yxt


Resolution: 2.4→47.2 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 3233 5.09 %
Rwork0.2089 --
obs0.2113 63558 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9439 0 304 139 9882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029897
X-RAY DIFFRACTIONf_angle_d0.5513384
X-RAY DIFFRACTIONf_dihedral_angle_d21.4663682
X-RAY DIFFRACTIONf_chiral_restr0.0431530
X-RAY DIFFRACTIONf_plane_restr0.0031703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.4161220.34062594X-RAY DIFFRACTION99
2.44-2.470.34671610.31942544X-RAY DIFFRACTION99
2.47-2.510.34681380.30482633X-RAY DIFFRACTION100
2.51-2.560.33311300.27532595X-RAY DIFFRACTION100
2.56-2.60.28721310.2672629X-RAY DIFFRACTION100
2.6-2.650.32711350.2832617X-RAY DIFFRACTION100
2.65-2.710.34851300.29482572X-RAY DIFFRACTION100
2.71-2.770.31431330.28762657X-RAY DIFFRACTION100
2.77-2.830.35541310.28082604X-RAY DIFFRACTION100
2.83-2.90.32271510.25292616X-RAY DIFFRACTION100
2.9-2.980.31051640.24922586X-RAY DIFFRACTION100
2.98-3.070.28821250.252597X-RAY DIFFRACTION100
3.07-3.170.31161230.24522642X-RAY DIFFRACTION100
3.17-3.280.27651590.24172623X-RAY DIFFRACTION99
3.28-3.410.27071360.22562593X-RAY DIFFRACTION100
3.41-3.570.27011380.21692647X-RAY DIFFRACTION100
3.57-3.760.23821370.19362613X-RAY DIFFRACTION100
3.76-3.990.21761490.18732634X-RAY DIFFRACTION100
3.99-4.30.21711550.17452605X-RAY DIFFRACTION99
4.3-4.730.19881360.15032639X-RAY DIFFRACTION99
4.73-5.410.23391460.17362651X-RAY DIFFRACTION99
5.41-6.820.23181470.20772684X-RAY DIFFRACTION99
6.82-47.20.22631560.18252750X-RAY DIFFRACTION99

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