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- PDB-5e3s: Crystal structure of Phosphatidylinositol-4-phosphate 5-kinase -

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Basic information

Entry
Database: PDB / ID: 5e3s
TitleCrystal structure of Phosphatidylinositol-4-phosphate 5-kinase
ComponentsPhosphatidylinositol-4-phosphate 5-kinase, type I, alpha
KeywordsTRANSFERASE / kinase
Function / homology
Function and homology information


Synthesis of PIPs at the plasma membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 1-phosphatidylinositol-4-phosphate 5-kinase / lipid kinase activity / 1-phosphatidylinositol-4-phosphate 5-kinase activity / phosphatidylinositol phosphate biosynthetic process / phosphorylation / ATP binding / metal ion binding / plasma membrane
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-4-phosphate 5-kinase type-1 gamma
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsMuftuoglu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Mechanism of substrate specificity of phosphatidylinositol phosphate kinases.
Authors: Muftuoglu, Y. / Xue, Y. / Gao, X. / Wu, D. / Ha, Y.
History
DepositionOct 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha


Theoretical massNumber of molelcules
Total (without water)42,2551
Polymers42,2551
Non-polymers00
Water00
1
A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha

A: Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha


Theoretical massNumber of molelcules
Total (without water)84,5112
Polymers84,5112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area1760 Å2
ΔGint-11 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.931, 88.931, 154.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phosphatidylinositol-4-phosphate 5-kinase, type I, alpha / Uncharacterized protein


Mass: 42255.422 Da / Num. of mol.: 1 / Fragment: unp residues 56-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: pip5k1aa, pip5k1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q503I3

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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: 3.62 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Peg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 11844 / Num. obs: 11844 / % possible obs: 100 % / Redundancy: 9.3 % / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
RefinementResolution: 3.1→39.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.881 / SU B: 15.291 / SU ML: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.724 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 562 4.8 %RANDOM
Rwork0.2101 ---
obs0.2129 11256 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 213.35 Å2 / Biso mean: 82.785 Å2 / Biso min: 41.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å2-0 Å2
2--1.14 Å2-0 Å2
3----2.28 Å2
Refinement stepCycle: final / Resolution: 3.1→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 0 2327
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192380
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.9623230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99423.107103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.61415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9961515
X-RAY DIFFRACTIONr_chiral_restr0.1160.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211841
X-RAY DIFFRACTIONr_mcbond_it7.5998.8931232
X-RAY DIFFRACTIONr_mcangle_it11.35713.2761533
X-RAY DIFFRACTIONr_scbond_it9.1728.7211148
LS refinement shellResolution: 3.099→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 38 -
Rwork0.271 825 -
all-863 -
obs--99.42 %

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