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- PDB-5lx2: Lt 14-3-3 in complex with PI4KIIIB peptide -

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Basic information

Entry
Database: PDB / ID: 5lx2
TitleLt 14-3-3 in complex with PI4KIIIB peptide
Components
  • KLTH0G14146p
  • Phosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE / phosphoserin / kinase / regulation
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding / receptor-mediated endocytosis / kinase activity / mitochondrial outer membrane / endosome / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site ...: / PI4KB/PIK1, accessory (PIK) domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphatidylinositol 4-kinase beta / KLTH0G14146p / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.579 Å
AuthorsBoura, E. / Eisenreichova, A.
CitationJournal: To Be Published
Title: Lt 14-3-3 in complex with PI4KIIIB peptide
Authors: Boura, E. / Eisenreichova, A.
History
DepositionSep 19, 2016Deposition site: PDBE / Processing site: PDBE
SupersessionNov 16, 2016ID: 5LI5
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)29,3022
Polymers29,3022
Non-polymers00
Water54030
1
A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta

A: KLTH0G14146p
B: Phosphatidylinositol 4-kinase beta


Theoretical massNumber of molelcules
Total (without water)58,6034
Polymers58,6034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3900 Å2
ΔGint-22 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.063, 123.671, 38.688
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 KLTH0G14146p


Mass: 28603.861 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (strain ATCC 56472 / CBS 6340 / NRRL Y-8284) (fungus)
Gene: KLTH0G14146g / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C5DN49
#2: Protein/peptide Phosphatidylinositol 4-kinase beta


Mass: 697.651 Da / Num. of mol.: 1 / Fragment: UNP residues 304-309 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A0B4J1S8, UniProt: Q9UBF8*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: MES, PEG 8000, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.579→44.49 Å / Num. obs: 10043 / % possible obs: 98.35 % / Redundancy: 3.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.1671 / Net I/σ(I): 6.5
Reflection shellResolution: 2.579→2.671 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.56 / CC1/2: 0.506 / % possible all: 98.25

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHO

5lho
PDB Unreleased entry


Resolution: 2.579→44.491 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 503 5.01 %
Rwork0.2027 --
obs0.2057 10040 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.579→44.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 0 30 1927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021927
X-RAY DIFFRACTIONf_angle_d0.5242608
X-RAY DIFFRACTIONf_dihedral_angle_d11.443716
X-RAY DIFFRACTIONf_chiral_restr0.023299
X-RAY DIFFRACTIONf_plane_restr0.002333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5788-2.83820.36671210.27342291X-RAY DIFFRACTION98
2.8382-3.24880.32171240.25312358X-RAY DIFFRACTION98
3.2488-4.09270.22921250.18522371X-RAY DIFFRACTION99
4.0927-44.49750.23561330.17662517X-RAY DIFFRACTION98

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