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

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Basic information

Entry
Database: PDB / ID: 4pla
TitleCrystal structure of phosphatidyl inositol 4-kinase II alpha in complex with ATP
ComponentsChimera protein of Phosphatidylinositol 4-kinase type 2-alpha and Lysozyme
KeywordsTRANSFERASE / HYDROLASE / phosphatidyl inositol / 4-kinase / ATP / lipid
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 / presynaptic membrane / lysozyme / lysozyme activity / perikaryon / cytoplasmic vesicle / early endosome membrane / host cell cytoplasm / endosome / neuron projection / defense response to bacterium / membrane raft / lysosomal membrane / phosphorylation / Golgi membrane / dendrite / neuronal cell body / magnesium ion binding / mitochondrion / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Type II phosphatidylinositol 4-kinase Lsb6/PI4K2 / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Endolysin / Phosphatidylinositol 4-kinase type 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.771 Å
AuthorsBaumlova, A. / Chalupska, D. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
MarieCurie FP7-PEOPLE-2012-CIG333916
CitationJournal: Embo Rep. / Year: 2014
Title: The crystal structure of the phosphatidylinositol 4-kinase II alpha.
Authors: Baumlova, A. / Chalupska, D. / Rozycki, B. / Jovic, M. / Wisniewski, E. / Klima, M. / Dubankova, A. / Kloer, D.P. / Nencka, R. / Balla, T. / Boura, E.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of Phosphatidylinositol 4-kinase type 2-alpha and Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2553
Polymers63,2411
Non-polymers1,0142
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.744, 79.539, 78.704
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 Chimera protein of Phosphatidylinositol 4-kinase type 2-alpha and Lysozyme / / 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, e, T4Tp126 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Star
References: UniProt: Q9BTU6, UniProt: D9IEF7, 1-phosphatidylinositol 4-kinase, lysozyme
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% PEG 4000, 150 mM (NH4)2SO4, 100 mM MES, pH = 6.5, 10 mM betaine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.77→36.84 Å / Num. obs: 16256 / % possible obs: 93.87 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 23.81

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.771→36.838 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 810 5 %Random
Rwork0.2115 ---
obs0.2135 16189 93.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.771→36.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 62 1 3951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134043
X-RAY DIFFRACTIONf_angle_d1.4215494
X-RAY DIFFRACTIONf_dihedral_angle_d17.3261512
X-RAY DIFFRACTIONf_chiral_restr0.095594
X-RAY DIFFRACTIONf_plane_restr0.009700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7709-2.94440.3351330.26682536X-RAY DIFFRACTION94
2.9444-3.17160.33621350.26162553X-RAY DIFFRACTION95
3.1716-3.49060.29911350.232564X-RAY DIFFRACTION95
3.4906-3.99520.27361340.19532541X-RAY DIFFRACTION94
3.9952-5.03150.17311340.18522563X-RAY DIFFRACTION93
5.0315-36.84120.22821390.2032622X-RAY DIFFRACTION91

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