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- PDB-4yc4: Crystal structure of phosphatidyl inositol 4-kinase II alpha in c... -

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Basic information

Entry
Database: PDB / ID: 4yc4
TitleCrystal structure of phosphatidyl inositol 4-kinase II alpha in complex with nucleotide analog
ComponentsPhosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha
KeywordsTRANSFERASE / Kinase / Complex / Inhibitor
Function / homology
Function and homology information


growing cell tip / AP-3 adaptor complex binding / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane ...growing cell tip / AP-3 adaptor complex binding / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / trans-Golgi network / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / presynaptic membrane / early endosome membrane / cytoplasmic vesicle / perikaryon / host cell cytoplasm / endosome membrane / endosome / defense response to bacterium / neuron projection / membrane raft / lysosomal membrane / Golgi membrane / neuronal cell body / dendrite / magnesium ion binding / mitochondrion / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Type II phosphatidylinositol 4-kinase Lsb6/PI4K2 / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-M59 / Endolysin / Phosphatidylinositol 4-kinase type 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.58 Å
AuthorsKlima, M. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicInterBioMed LO1302 Czech Republic
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a ...Title: The high-resolution crystal structure of phosphatidylinositol 4-kinase II beta and the crystal structure of phosphatidylinositol 4-kinase II alpha containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design.
Authors: Klima, M. / Baumlova, A. / Chalupska, D. / Hrebabecky, H. / Dejmek, M. / Nencka, R. / Boura, E.
History
DepositionFeb 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 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: Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9273
Polymers63,2411
Non-polymers6872
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint1 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.414, 103.770, 78.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphatidylinositol 4-kinase type 2-alpha,Lysozyme,Phosphatidylinositol 4-kinase type 2-alpha / Phosphatidylinositol 4-kinase type II-alpha


Mass: 63240.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PI4K2A, T4Tp126 / Plasmid: pRSFD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star
References: UniProt: Q9BTU6, UniProt: D9IEF7, 1-phosphatidylinositol 4-kinase, lysozyme
#2: Chemical ChemComp-M59 / [(1S,3S,4S)-3-(6-amino-9H-purin-9-yl)bicyclo[2.2.1]hept-1-yl]methanol


Mass: 259.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N5O
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH = 7.0, 10% w/v PEG 4000, 10% v/v 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.58→49.07 Å / Num. obs: 20124 / % possible obs: 95.77 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.0714 / Net I/σ(I): 15.98
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.36 / % possible all: 74.15

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2.58→49.068 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 1007 5 %
Rwork0.214 --
obs0.2162 20124 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→49.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 46 3 3931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124022
X-RAY DIFFRACTIONf_angle_d1.6725466
X-RAY DIFFRACTIONf_dihedral_angle_d16.0841500
X-RAY DIFFRACTIONf_chiral_restr0.106595
X-RAY DIFFRACTIONf_plane_restr0.012703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.577-2.71280.36571140.29152158X-RAY DIFFRACTION77
2.7128-2.88280.31431390.26772651X-RAY DIFFRACTION95
2.8828-3.10530.31231470.25842794X-RAY DIFFRACTION100
3.1053-3.41780.31611490.23852823X-RAY DIFFRACTION100
3.4178-3.91210.26291490.20542836X-RAY DIFFRACTION100
3.9121-4.92810.19541510.18162872X-RAY DIFFRACTION100
4.9281-49.0770.22971580.19492983X-RAY DIFFRACTION99

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