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- PDB-5eut: Crystal structure of phosphatidyl inositol 4-kinase II alpha in t... -

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Basic information

Entry
Database: PDB / ID: 5eut
TitleCrystal structure of phosphatidyl inositol 4-kinase II alpha in the apo state
ComponentsPhosphatidylinositol 4-kinase type 2-alpha,Endolysin,Phosphatidylinositol 4-kinase type 2-alpha
KeywordsTRANSFERASE / kinase / lipid / phosphatidylinositol
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 / 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-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
Endolysin / Phosphatidylinositol 4-kinase type 2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.802 Å
AuthorsBaumlova, A. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLO1302 Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of phosphatidyl inositol 4-kinase II alpha in the apo state
Authors: Baumlova, A. / Boura, E.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 4-kinase type 2-alpha,Endolysin,Phosphatidylinositol 4-kinase type 2-alpha


Theoretical massNumber of molelcules
Total (without water)63,2411
Polymers63,2411
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.006, 101.515, 78.135
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,Endolysin,Phosphatidylinositol 4-kinase type 2-alpha / Phosphatidylinositol 4-kinase type II-alpha / Lysis protein / Lysozyme / Muramidase / ...Phosphatidylinositol 4-kinase type II-alpha / Lysis protein / Lysozyme / Muramidase / 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 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BTU6, UniProt: P00720, 1-phosphatidylinositol 4-kinase, lysozyme

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1 M bicine/Trizma base pH 8.5
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.802→48.97 Å / Num. obs: 16220 / % possible obs: 99.22 % / Redundancy: 7.07 % / Net I/σ(I): 8.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.802→48.967 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2889 805 5.01 %Random selection
Rwork0.2464 ---
obs0.2486 16072 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.802→48.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 0 0 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033984
X-RAY DIFFRACTIONf_angle_d0.9055403
X-RAY DIFFRACTIONf_dihedral_angle_d14.7961489
X-RAY DIFFRACTIONf_chiral_restr0.036588
X-RAY DIFFRACTIONf_plane_restr0.007702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8017-2.97720.41491290.41982436X-RAY DIFFRACTION96
2.9772-3.2070.35111320.34192517X-RAY DIFFRACTION100
3.207-3.52960.36291330.31182512X-RAY DIFFRACTION100
3.5296-4.04020.32161330.25162538X-RAY DIFFRACTION100
4.0402-5.08940.27291360.21492574X-RAY DIFFRACTION100
5.0894-48.9740.22771420.19552690X-RAY DIFFRACTION100

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