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- PDB-1bo1: PHOSPHATIDYLINOSITOL PHOSPHATE KINASE TYPE II BETA -

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Basic information

Entry
Database: PDB / ID: 1bo1
TitlePHOSPHATIDYLINOSITOL PHOSPHATE KINASE TYPE II BETA
ComponentsPROTEIN (PHOSPHATIDYLINOSITOL PHOSPHATE KINASE IIBETA)
KeywordsTRANSFERASE / LIPID SIGNALING
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 / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane ...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 / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / negative regulation of insulin receptor signaling pathway / autophagosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / regulation of autophagy / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 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 Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 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 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3 Å
AuthorsRao, V.D. / Misra, S. / Boronenkov, I.V. / Anderson, R.A. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Structure of type IIbeta phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation.
Authors: Rao, V.D. / Misra, S. / Boronenkov, I.V. / Anderson, R.A. / Hurley, J.H.
History
DepositionAug 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PHOSPHATIDYLINOSITOL PHOSPHATE KINASE IIBETA)
B: PROTEIN (PHOSPHATIDYLINOSITOL PHOSPHATE KINASE IIBETA)


Theoretical massNumber of molelcules
Total (without water)94,8962
Polymers94,8962
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.915, 182.403, 106.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.996792, 0.067419, -0.043137), (-0.029964, -0.814091, -0.579964), (-0.074218, -0.576811, 0.813499)
Vector: 78.7441, 81.5331, 28.7918)

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Components

#1: Protein PROTEIN (PHOSPHATIDYLINOSITOL PHOSPHATE KINASE IIBETA) / PIPK


Mass: 47447.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HUMAN ENZYME CLONED INTO E.COLI. / Plasmid: PET28B / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: P78356, 1-phosphatidylinositol-4-phosphate 5-kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.6
Details: 100MM SODIUM CITRATE PH5.6 200MM MAGNESIUM ACETATE 100MM LITHIUM ACETATE 16% PEG (4000)
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH5.6
2200 mMmagnesium acetate1reservoir
3100 mMlithium acetate1reservoir
413-17 %PEG40001reservoir
513-17 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 21621 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rsym value: 0.052 / Net I/σ(I): 14.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.325 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 297963 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: SIRAS / Resolution: 3→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 95 5 %RANDOM
Rwork0.229 ---
obs0.229 17398 94.9 %-
Displacement parametersBiso mean: 48.05 Å2
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 0 20 5161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.339
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.12 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3098 95 5 %
Rwork0.254 1990 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.455
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.726
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.339
LS refinement shell
*PLUS
% reflection Rfree: 5 %

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