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- PDB-9hhm: Crystal structure of phosphatidyl inositol 4-kinase II beta in co... -

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Basic information

Entry
Database: PDB / ID: 9hhm
TitleCrystal structure of phosphatidyl inositol 4-kinase II beta in complex with HH5129
ComponentsPhosphatidylinositol 4-kinase type 2-beta,Endolysin
KeywordsTRANSFERASE / lipid / kinase / inhibitor / PI4K2B / PI4P
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 / phosphatidylinositol phosphate biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane ...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 / phosphatidylinositol phosphate biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / 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 / 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
: / 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: 2.25 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of phosphatidyl inositol 4-kinase II beta in complex with HH5129
Authors: Klima, M. / Boura, E.
History
DepositionNov 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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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
B: Phosphatidylinositol 4-kinase type 2-beta,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5554
Polymers119,2262
Non-polymers1,3292
Water2,954164
1
A: Phosphatidylinositol 4-kinase type 2-beta,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2782
Polymers59,6131
Non-polymers6641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 4-kinase type 2-beta,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2782
Polymers59,6131
Non-polymers6641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.240, 105.240, 211.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 59613.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Kinase domain of human PI4K2B (residues 90-450) with cystein-rich loop (residues 165-175) replaced with T4 lysozyme.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PI4K2B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8TCG2, UniProt: P00720, 1-phosphatidylinositol 4-kinase, lysozyme
#2: Chemical ChemComp-A1IVA / (1~{S},2~{S},4~{S},5~{R})-6-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-bis(oxidanylidene)-$l^{6}-phosphanyl]methyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxycyclohexane-1,2,3,4,5-pentol


Mass: 664.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N5O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES, pH 7.0; 15 % (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→39.27 Å / Num. obs: 57107 / % possible obs: 99.79 % / Redundancy: 23.7 % / Biso Wilson estimate: 52.35 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2754 / Rpim(I) all: 0.05681 / Rrim(I) all: 0.2815 / Net I/σ(I): 8.55
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 15.9 % / Rmerge(I) obs: 3.199 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 5550 / CC1/2: 0.516 / CC star: 0.825 / Rpim(I) all: 0.7491 / Rrim(I) all: 3.293 / % possible all: 98.51

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Processing

Software
NameVersionClassification
XDSxdsgui2data reduction
XDSxdsgui2data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→39.27 Å / SU ML: 0.3076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 2855 5 %random selection
Rwork0.2158 54241 --
obs0.217 57096 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.75 Å2
Refinement stepCycle: LAST / Resolution: 2.25→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7193 0 73 164 7430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227471
X-RAY DIFFRACTIONf_angle_d0.491410141
X-RAY DIFFRACTIONf_chiral_restr0.041099
X-RAY DIFFRACTIONf_plane_restr0.00411304
X-RAY DIFFRACTIONf_dihedral_angle_d11.63912776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.32561370.30752607X-RAY DIFFRACTION97.03
2.29-2.330.32111400.28922666X-RAY DIFFRACTION100
2.33-2.380.3021400.2812652X-RAY DIFFRACTION100
2.38-2.420.2981400.27322672X-RAY DIFFRACTION100
2.42-2.480.35321410.27082665X-RAY DIFFRACTION100
2.48-2.530.27641410.25162681X-RAY DIFFRACTION100
2.53-2.60.25221410.24522683X-RAY DIFFRACTION100
2.6-2.670.30631410.2522680X-RAY DIFFRACTION100
2.67-2.750.30421410.25952684X-RAY DIFFRACTION100
2.75-2.830.29541420.25812698X-RAY DIFFRACTION100
2.83-2.940.30571420.24332700X-RAY DIFFRACTION100
2.94-3.050.2481420.2392686X-RAY DIFFRACTION100
3.05-3.190.2741430.24232715X-RAY DIFFRACTION100
3.19-3.360.28461430.25432714X-RAY DIFFRACTION100
3.36-3.570.22271420.22492707X-RAY DIFFRACTION100
3.57-3.850.24471440.20082736X-RAY DIFFRACTION100
3.85-4.230.19891460.18382763X-RAY DIFFRACTION100
4.23-4.840.19461450.17552763X-RAY DIFFRACTION100
4.85-6.10.21181480.20552809X-RAY DIFFRACTION100
6.1-39.270.22021560.19392960X-RAY DIFFRACTION99.46

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