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- PDB-8omi: Crystal structure of the inositol hexakisphosphate kinase EhIP6KA... -

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Basic information

Entry
Database: PDB / ID: 8omi
TitleCrystal structure of the inositol hexakisphosphate kinase EhIP6KA M85 variant in complex with ATP and Mg2+
ComponentsKinase
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / phosphatidylinositol phosphate biosynthetic process / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Kinase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSchuetz, A. / Aguirre, T. / Fiedler, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Research Foundation (DFG)EXC 2008-390540038 Germany
CitationJournal: Elife / Year: 2023
Title: An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor.
Authors: Aguirre, T. / Dornan, G.L. / Hostachy, S. / Neuenschwander, M. / Seyffarth, C. / Haucke, V. / Schutz, A. / von Kries, J.P. / Fiedler, D.
History
DepositionMar 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0697
Polymers29,3331
Non-polymers7366
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-22 kcal/mol
Surface area12070 Å2
Unit cell
Length a, b, c (Å)102.820, 102.820, 111.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Kinase


Mass: 29332.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI7A_103520 / Production host: Escherichia coli (E. coli)
References: UniProt: N9UNA8, Transferases; Transferring phosphorus-containing groups

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 1 mM MgCl2, 460 mM NaH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.77→37.81 Å / Num. obs: 29205 / % possible obs: 99.15 % / Redundancy: 7.5 % / Biso Wilson estimate: 30.96 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.61
Reflection shellResolution: 1.773→1.837 Å / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2811 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→37.81 Å / SU ML: 0.3136 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 1449 5 %
Rwork0.2308 27544 -
obs0.232 28993 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.18 Å2
Refinement stepCycle: LAST / Resolution: 1.77→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 45 189 2233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222087
X-RAY DIFFRACTIONf_angle_d0.54112807
X-RAY DIFFRACTIONf_chiral_restr0.0448297
X-RAY DIFFRACTIONf_plane_restr0.0034347
X-RAY DIFFRACTIONf_dihedral_angle_d11.2282267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.840.42331400.38652671X-RAY DIFFRACTION98.25
1.84-1.910.42511420.40032687X-RAY DIFFRACTION98.4
1.91-20.42561430.35752725X-RAY DIFFRACTION98.96
2-2.10.37991430.30422718X-RAY DIFFRACTION99.17
2.1-2.230.33071450.28592743X-RAY DIFFRACTION99.35
2.23-2.410.27651430.26532722X-RAY DIFFRACTION99.41
2.41-2.650.28431450.24962757X-RAY DIFFRACTION99.21
2.65-3.030.29371460.23562780X-RAY DIFFRACTION99.56
3.03-3.820.21821480.2052814X-RAY DIFFRACTION99.7
3.82-37.810.18291540.17582927X-RAY DIFFRACTION99.64

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