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- PDB-8oxe: Inositol 1,3,4-trisphosphate 5/6-kinase 1 from Solanum tuberosum ... -

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Basic information

Entry
Database: PDB / ID: 8oxe
TitleInositol 1,3,4-trisphosphate 5/6-kinase 1 from Solanum tuberosum (StITPK1) in complex with ADP/Mg2+
ComponentsInositol-tetrakisphosphate 1-kinase
KeywordsTRANSFERASE / Inositol kinase
Function / homology
Function and homology information


inositol-tetrakisphosphate 1-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol trisphosphate metabolic process / magnesium ion binding / ATP binding
Similarity search - Function
Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFaba-Rodriguez, R. / Li, A.W.H. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: Biochemistry / Year: 2024
Title: Crystal Structure and Enzymology of Solanum tuberosum Inositol Tris/Tetrakisphosphate Kinase 1 ( St ITPK1).
Authors: Whitfield, H.L. / Rodriguez, R.F. / Shipton, M.L. / Li, A.W.H. / Riley, A.M. / Potter, B.V.L. / Hemmings, A.M. / Brearley, C.A.
History
DepositionMay 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3785
Polymers36,8771
Non-polymers5004
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-31 kcal/mol
Surface area16770 Å2
Unit cell
Length a, b, c (Å)89.610, 140.770, 55.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-402-

MG

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Components

#1: Protein Inositol-tetrakisphosphate 1-kinase


Mass: 36877.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: ipka / Production host: Escherichia coli (E. coli) / References: UniProt: A4H2J0
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M calcium chloride dihydrate, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→75.59 Å / Num. obs: 519292 / % possible obs: 99.69 % / Redundancy: 20 % / Biso Wilson estimate: 27.96 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.0434 / Rrim(I) all: 0.2088 / Net I/σ(I): 20.82
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 15 % / Num. unique obs: 50938 / CC1/2: 0.868 / CC star: 0.964 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
carelessdata reduction
carelessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→75.59 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2406 810 4.81 %
Rwork0.1898 16025 -
obs0.1923 16835 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.41 Å2
Refinement stepCycle: LAST / Resolution: 2.26→75.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 30 124 2598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032524
X-RAY DIFFRACTIONf_angle_d1.23263414
X-RAY DIFFRACTIONf_chiral_restr0.0687374
X-RAY DIFFRACTIONf_plane_restr0.0133436
X-RAY DIFFRACTIONf_dihedral_angle_d10.8736340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.40.27221190.2262619X-RAY DIFFRACTION99.35
2.4-2.590.29041320.21862614X-RAY DIFFRACTION99.35
2.59-2.850.27351380.21682642X-RAY DIFFRACTION99.75
2.85-3.260.24621470.20022648X-RAY DIFFRACTION99.96
3.26-4.110.2461190.17362701X-RAY DIFFRACTION99.96
4.11-75.590.20341550.16972801X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.512397611910.513143723227-1.089367402482.46273444812-1.064141940044.37095832121-0.08265080978430.05692971019010.0785880594260.1978181746640.1292311479820.3713155419470.0845061241137-0.417940782976-0.01675968314030.224893109827-0.005989287202150.002742913405680.165467568666-0.03062058904730.258370610205-28.2857116689-22.205236743336.6325519667
21.412604469370.216917330862-0.9777271598474.751617037891.672955479233.63332940938-0.1073736275670.264144327325-0.265985931347-0.5130684210940.0522116505798-0.3390356195360.2584176415090.005895130989540.02986682787710.213540696939-0.00759928722453-0.01295477687110.2140976297360.01798078135630.229135896447-13.3259212775-22.090330230914.061389901
33.23763496138-1.12258645260.6001184196294.117122993040.8762007928510.855772769209-0.134038900007-0.0215769195095-0.175915815231-0.06145967617420.125562188943-0.5286062394190.1025961301590.340454117223-0.09445687776750.302778072992-0.02725414386950.06571998365090.4205405338290.0192088887810.428423171265-0.573442703636-13.206441946118.0905575782
42.62357216037-0.101407381741-0.8398314960124.56080140484-1.038495758975.05536266543-0.01211369580910.01368683960920.1605307435760.27891794290.09017904581340.281975867032-0.225020342971-0.377239676922-0.05106466773310.183133015392-0.0101642201484-0.04140236426290.118739214299-0.0246675764880.233879488856-24.2757623698-10.742466689829.9544893378
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 119 )8 - 1191 - 112
22chain 'A' and (resid 120 through 203 )120 - 203113 - 196
33chain 'A' and (resid 204 through 251 )204 - 251197 - 233
44chain 'A' and (resid 252 through 320 )252 - 320234 - 302

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