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- PDB-4wtv: Crystal structure of the phosphatidylinositol 4-kinase IIbeta -

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Basic information

Entry
Database: PDB / ID: 4wtv
TitleCrystal structure of the phosphatidylinositol 4-kinase IIbeta
ComponentsPhosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
KeywordsTRANSFERASE / lipid kinase / phosphatidyl inositol / hydrolase
Function / homology
Function and homology information


Synthesis of PIPs at the ER membrane / 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 ...Synthesis of PIPs at the ER membrane / 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 / early endosome membrane / host cell cytoplasm / endosome / defense response to bacterium / phosphorylation / Golgi membrane / endoplasmic reticulum membrane / 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-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKlima, M. / Baumlova, A. / Chalupska, D. / Boura, E.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
MarieCurieFP7-PEOPLE-2012-CIG, project number 333916 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
DepositionOct 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
B: Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7504
Polymers118,7362
Non-polymers1,0142
Water5,026279
1
A: Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8752
Polymers59,3681
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8752
Polymers59,3681
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.010, 106.010, 214.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta / Phosphatidylinositol 4-kinase type II-beta / PI4KII-BETA / Lysis protein / Lysozyme / Muramidase / ...Phosphatidylinositol 4-kinase type II-beta / PI4KII-BETA / Lysis protein / Lysozyme / Muramidase / Phosphatidylinositol 4-kinase type II-beta / PI4KII-BETA


Mass: 59367.898 Da / Num. of mol.: 2
Fragment: UNP residues 90-165,UNP residues 2-164,UNP residues 176-450,UNP residues 90-165,UNP residues 2-164,UNP residues 176-450,UNP residues 90-165,UNP residues 2-164,UNP residues 176-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PI4K2B / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8TCG2, UniProt: P00720, 1-phosphatidylinositol 4-kinase, lysozyme
#2: Chemical ChemComp-ATP / ADENOSINE-5'-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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/Imidazole pH = 6.5, 10% w/v PEG 4000, 20% v/v glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.28272 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28272 Å / Relative weight: 1
ReflectionResolution: 1.9→47.52 Å / Num. obs: 96773 / % possible obs: 99.98 % / Redundancy: 17.6 % / Rmerge(I) obs: 0.1002 / Rsym value: 0.1032 / Net I/σ(I): 17.42
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 17.4 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSJanuary 10, 2014data reduction
Coot0.7.2model building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLA

4pla


Resolution: 1.9→47.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2404 4839 5 %
Rwork0.2088 --
obs0.2104 96762 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6947 0 62 279 7288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017313
X-RAY DIFFRACTIONf_angle_d1.2469953
X-RAY DIFFRACTIONf_dihedral_angle_d15.8522671
X-RAY DIFFRACTIONf_chiral_restr0.0411074
X-RAY DIFFRACTIONf_plane_restr0.0051267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.32881580.2993000X-RAY DIFFRACTION100
1.9216-1.94420.36381590.28593020X-RAY DIFFRACTION100
1.9442-1.96790.30271590.27323017X-RAY DIFFRACTION100
1.9679-1.99280.30061590.26763024X-RAY DIFFRACTION100
1.9928-2.0190.30241570.26952993X-RAY DIFFRACTION100
2.019-2.04670.30181610.25883061X-RAY DIFFRACTION100
2.0467-2.07590.28431590.25733008X-RAY DIFFRACTION100
2.0759-2.10690.3471580.25333014X-RAY DIFFRACTION100
2.1069-2.13990.29761600.23633038X-RAY DIFFRACTION100
2.1399-2.17490.26841600.23913031X-RAY DIFFRACTION100
2.1749-2.21240.27291590.23443030X-RAY DIFFRACTION100
2.2124-2.25270.2721600.23913045X-RAY DIFFRACTION100
2.2527-2.2960.29371600.22893026X-RAY DIFFRACTION100
2.296-2.34290.26581600.23573041X-RAY DIFFRACTION100
2.3429-2.39380.27091590.23033032X-RAY DIFFRACTION100
2.3938-2.44950.28651600.22313033X-RAY DIFFRACTION100
2.4495-2.51070.26971600.22493043X-RAY DIFFRACTION100
2.5107-2.57860.23351620.21753082X-RAY DIFFRACTION100
2.5786-2.65450.28421610.2293044X-RAY DIFFRACTION100
2.6545-2.74020.26481590.23213035X-RAY DIFFRACTION100
2.7402-2.83810.2861610.2323058X-RAY DIFFRACTION100
2.8381-2.95170.27071630.23043091X-RAY DIFFRACTION100
2.9517-3.0860.25321610.23463059X-RAY DIFFRACTION100
3.086-3.24870.26071630.2353089X-RAY DIFFRACTION100
3.2487-3.45220.28411620.23043091X-RAY DIFFRACTION100
3.4522-3.71860.21831630.19973101X-RAY DIFFRACTION100
3.7186-4.09260.21971650.17613136X-RAY DIFFRACTION100
4.0926-4.68440.17641660.15393137X-RAY DIFFRACTION100
4.6844-5.90010.1741670.16893190X-RAY DIFFRACTION100
5.9001-47.53460.20211780.18843354X-RAY DIFFRACTION100

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