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- PDB-2ybx: Crystal Structure of Human Phosphatidylinositol-5-phosphate 4-kin... -

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Basic information

Entry
Database: PDB / ID: 2ybx
TitleCrystal Structure of Human Phosphatidylinositol-5-phosphate 4-kinase type-2 alpha
ComponentsPHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA
KeywordsTRANSFERASE / KINASE / SIGNALLING
Function / homology
Function and homology information


vesicle-mediated cholesterol transport / 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 / megakaryocyte development / phosphatidylinositol phosphate biosynthetic process ...vesicle-mediated cholesterol transport / 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 / megakaryocyte development / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / photoreceptor outer segment / photoreceptor inner segment / negative regulation of insulin receptor signaling pathway / autophagosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / regulation of autophagy / protein homodimerization activity / nucleoplasm / ATP binding / 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
PHOSPHATE ION / Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsTresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. ...Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Siponen, M.I. / Thorsell, A.G. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
CitationJournal: To be Published
Title: Crystal Structure of Human Phosphatidylinositol-5-Phosphate 4-Kinase Type-2 Alpha
Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / ...Authors: Tresaugues, L. / Moche, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Graslund, S. / Karlberg, T. / Kotenyova, T. / Kouznetsova, E. / Nyman, T. / Persson, C. / Schuler, H. / Siponen, M.I. / Thorsell, A.G. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
History
DepositionMar 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA
B: PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7213
Polymers90,6262
Non-polymers951
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-13.8 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.040, 98.508, 104.879
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99988, 0.01034, -0.01175), (0.0059, 0.94451, 0.32844), (0.0145, 0.32833, -0.94445)
Vector: -28.93359, -6.85638, 41.15516)

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Components

#1: Protein PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE-2 ALPHA / 1-PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE 2-ALPHA / DIPHOSPHOINOSITIDE KINASE 2-ALPHA / PIP5KIII ...1-PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE 2-ALPHA / DIPHOSPHOINOSITIDE KINASE 2-ALPHA / PIP5KIII / PHOSPHATIDYLINOSITOL-5-PHOSPHATE 4-KINASE TYPE II ALPHA / PI(5)P 4-KINASE TYPE II ALPHA / PIP4KII-ALPHA / PTDINS(4)P-5-KINASE B ISOFORM / PTDINS(4)P-5-KINASE C ISOFORM / PTDINS(5)P-4-KINASE ISOFORM 2-ALPHA


Mass: 45312.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-405
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYL-ASPARTATE INTERMEDIATE IN POSITION 359 / Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3 PRARE
References: UniProt: P48426, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M MAGNESIUM FORMATE, 16% PEG3350, 2 MM BENZYL(1,3,5)TRIPHOSPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.56→28.47 Å / Num. obs: 28302 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 55.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.1 / % possible all: 96.8

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BO1

1bo1


Resolution: 2.56→28.37 Å / Cor.coef. Fo:Fc: 0.8973 / Cor.coef. Fo:Fc free: 0.8661 / SU R Cruickshank DPI: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.401 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.267
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1444 5.11 %RANDOM
Rwork0.1881 ---
obs0.1907 28285 97.94 %-
Displacement parametersBiso mean: 49.11 Å2
Baniso -1Baniso -2Baniso -3
1-15.5792 Å20 Å2-4.0507 Å2
2---21.349 Å20 Å2
3---5.7697 Å2
Refine analyzeLuzzati coordinate error obs: 0.314 Å
Refinement stepCycle: LAST / Resolution: 2.56→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 5 121 5336
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015362HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077245HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2508SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes759HARMONIC5
X-RAY DIFFRACTIONt_it5362HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion3.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion677SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6124SEMIHARMONIC4
LS refinement shellResolution: 2.56→2.66 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.28 147 5.04 %
Rwork0.2315 2769 -
all0.2339 2916 -
obs--97.94 %

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