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- PDB-2gk9: Human Phosphatidylinositol-4-phosphate 5-kinase, type II, gamma -

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Basic information

Entry
Database: PDB / ID: 2gk9
TitleHuman Phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
Componentsphosphatidylinositol-4-phosphate 5-kinase, type II, gamma
KeywordsTRANSFERASE / phosphoinositide / kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / intracellular organelle / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / intracellular organelle / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phosphorylation / endoplasmic reticulum / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / : / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. ...Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / : / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsUppenberg, J. / Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Uppenberg, J. / Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Holmberg-Schiavone, L. / Edwards, A. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Hallberg, B.M. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Human Phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
Authors: Thorsell, A.G. / Uppenberg, J. / Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Thorsell, A.G. / Uppenberg, J. / Hogbom, M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Van Den Berg, S. / Weigelt, J. / Holmberg-Schiavone, L. / Persson, C. / Hallberg, B.M.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
B: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
C: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
D: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma


Theoretical massNumber of molelcules
Total (without water)178,7674
Polymers178,7674
Non-polymers00
Water0
1
A: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
D: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma


Theoretical massNumber of molelcules
Total (without water)89,3842
Polymers89,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-10 kcal/mol
Surface area27330 Å2
MethodPISA
2
B: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma
C: phosphatidylinositol-4-phosphate 5-kinase, type II, gamma


Theoretical massNumber of molelcules
Total (without water)89,3842
Polymers89,3842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-9 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.390, 95.390, 189.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
phosphatidylinositol-4-phosphate 5-kinase, type II, gamma /


Mass: 44691.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP5K2C / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q8TBX8, 1-phosphatidylinositol-4-phosphate 5-kinase

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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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % Peg3350 0.3 M di-ammoniumtartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.953 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2005
RadiationMonochromator: Double crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 41535 / Num. obs: 40823 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.55 % / Rsym value: 0.0791 / Net I/σ(I): 8.23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.13 / % possible all: 99.7

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
MOLREPphasing
SHELXL-97refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cross valid method: Rfree / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: No twin reflections in same set. TWIN OPERATOR= h,-k,-l ; and twin fraction = 0.50
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1890 -NO TWIN REFLECTIONS
Rwork0.254 ---
all0.261 39963 --
obs0.261 39963 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8233 0 0 0 8233

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