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- PDB-1e8x: STRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHA... -

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Entry
Database: PDB / ID: 1e8x
TitleSTRUCTURAL INSIGHTS INTO PHOSHOINOSITIDE 3-KINASE ENZYMATIC MECHANISM AND SIGNALLING
ComponentsPHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT
KeywordsPHOSPHOINOSITIDE 3-KINASE GAMMA / SECONDARY MESSENGER GENERATION / PI3K / PI 3K
Function / homologyPhosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-kinase, C2 domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain / Phosphatidylinositol 3-kinase, Vps34 type / Protein kinase-like domain superfamily / Phosphatidylinositol kinase / Armadillo-type fold / Phosphatidylinositol 3/4-kinase, conserved site / Ubiquitin-like domain superfamily ...Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-kinase, C2 domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain / Phosphatidylinositol 3-kinase, Vps34 type / Protein kinase-like domain superfamily / Phosphatidylinositol kinase / Armadillo-type fold / Phosphatidylinositol 3/4-kinase, conserved site / Ubiquitin-like domain superfamily / C2 domain superfamily / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphoinositide 3-kinase C2 / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3- and 4-kinases family profile. / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PIK helical domain profile. / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphatidylinositol 3-kinase C2 (PI3K C2) domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol-4,5-bisphosphate 3-kinase / immune system process / 1-phosphatidylinositol-4-phosphate 3-kinase activity / phosphatidylinositol-3-phosphate biosynthetic process / phosphatidylinositol 3-kinase complex / phosphatidylinositol phosphorylation / phosphatidylinositol 3-kinase signaling / 1-phosphatidylinositol-3-kinase activity / phosphatidylinositol-mediated signaling / endocytosis / chemotaxis / phosphatidylinositol-4,5-bisphosphate 3-kinase activity / cell migration / platelet activation / angiogenesis / non-specific serine/threonine protein kinase / inflammatory response / protein serine/threonine kinase activity / protein phosphorylation / membrane / ATP binding / plasma membrane / cytoplasm / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Function and homology information
Specimen sourceSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 2.2 Å resolution
AuthorsWalker, E.H. / Perisic, O. / Ried, C. / Stephens, L. / Williams, R.L.
Citation
Journal: Mol.Cell / Year: 2000
Title: Structural Determinations of Phosphoinositide 3-Kinase Inhibition by Wortmannin, Ly294002, Quercetin, Myricetin and Staurosporine
Authors: Walker, E.H. / Pacold, M.E. / Perisic, O. / Stephens, L. / Hawkins, P.T. / Whymann, M.P. / Williams, R.L.
#1: Journal: Nature / Year: 1999
Title: Structural Insights Into Phosphoinositide 3-Kinase Catalysis and Signalling
Authors: Walker, E.H. / Perisic, O. / Ried, C. / Stephens, L. / Williams, R.L.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 3, 2000 / Release: Oct 26, 2000
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 26, 2000Structure modelrepositoryInitial release
1.1May 8, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 24, 2018Structure modelData collection / Source and taxonomyentity_src_gen_entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_strain
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,03411
Polyers109,9531
Non-polymers2,08210
Water4,558253
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)143.288, 67.561, 106.952
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

#1: Protein/peptide PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT / PTDINS-3-KINASE P110 / PI3K


Mass: 109952.555 Da / Num. of mol.: 1 / Details: LUTETIUM DERIVATIVE / Fragment: PI3-KINASE P110 SUBUNIT GAMMA / Mutation: YES / Source: (gene. exp.) SUS SCROFA (pig) / Cell: NEUTROPHIL / Gene: P120S144C / Plasmid name: PACHLT-C / Gene (production host): P120S144C / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O02697, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 9 / Formula: Lu / Lutetium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Formula: H2O / Water
Sequence detailsFUTHER DATA COLLECTION AND REFINEMENT AFTER THE ORIGINAL DEPOSITION OF 1QMM SUGGESTED A REGISTER ...FUTHER DATA COLLECTION AND REFINEMENT AFTER THE ORIGINAL DEPOSITION OF 1QMM SUGGESTED A REGISTER SHIFT IN THE ELECTRON DENSITY IN THE RAS BINDING DOMAIN. THEREFORE THE ELECTRON DENSITY THAT USED TO CORRESPOND TO RESIDUES 231 TO 256 NOW CORRESPONDS TO RESIDUES 228 TO 253. THE NATIVE PROTEIN WAS MUTATED BY DELETION OF RESIDUES 1-143. THE RESIDUES 142 AND 143 LISTED HERE ARE FROM THE HIS-TAG, AFTER THROMBIN CLEAVAGE, ALSO RESEQUENCING OF THE CLONE SHOWED THAT ARG 505 IS ACTUALLY ALA.

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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: 2.6 / Density percent sol: 41 %
Crystal growpH: 7.25 / Details: 14% PEG 4000, 0.2 M LI2SO4, 0.1 M TRIS PH 7.25
Crystal grow
*PLUS
Temp: 17 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: used hair seeding
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
10.1 MTris1reservoir
2250 mMammonium sulfate1reservoir
319 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Type: ESRF BEAMLINE ID2 / Synchrotron site: ESRF / Beamline: ID2 / Wavelength: 0.988
DetectorType: MARRESEARCH / Details: BENT MIRROR / Detector: IMAGE PLATE / Collection date: May 15, 1999
RadiationMonochromator: SI(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 43.4 Å2 / D resolution high: 2.2 Å / D resolution low: 25 Å / Number obs: 49599 / Observed criterion sigma I: 0 / Rmerge I obs: 0.095 / NetI over sigmaI: 14.3 / Redundancy: 3.9 % / Percent possible obs: 95.5
Reflection shellRmerge I obs: 0.53 / Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / MeanI over sigI obs: 1.1 / Redundancy: 3.3 % / Percent possible all: 93.3

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Processing

Software
NameVersionClassification
SOLVEmodel building
SCALAdata scaling
CNS1.0phasing
SHARPphasing
SOLOMONphasing
SOLVEphasing
CNS1.0refinement
RefineMethod to determine structure: MIR
Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
R Free selection details: RANDOM / Data cutoff high absF: 2252673.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 70.8171 / Solvent model param ksol: 0.363152
Displacement parametersB iso mean: 62.4 Å2 / Aniso B11: -4.87 Å2 / Aniso B12: 0 Å2 / Aniso B13: -4.02 Å2 / Aniso B22: 5.25 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.38 Å2
Least-squares processR factor R free: 0.306 / R factor R free error: 0.006 / R factor R work: 0.255 / R factor obs: 0.255 / Highest resolution: 2.2 Å / Lowest resolution: 100 Å / Number reflection R free: 2776 / Number reflection obs: 49558 / Percent reflection R free: 5.6 / Percent reflection obs: 95.4
Refine analyzeLuzzati coordinate error free: 0.44 Å / Luzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.47 Å / Luzzati sigma a obs: 0.38 Å
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 100 Å
Number of atoms included #LASTProtein: 6805 / Nucleic acid: 0 / Ligand: 40 / Solvent: 253 / Total: 7098
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.881.5
X-RAY DIFFRACTIONc_mcangle_it4.302.0
X-RAY DIFFRACTIONc_scbond_it4.272.0
X-RAY DIFFRACTIONc_scangle_it5.592.5
Refine LS shellHighest resolution: 2.2 Å / R factor R free: 0.396 / R factor R free error: 0.019 / R factor R work: 0.366 / Lowest resolution: 2.34 Å / Number reflection R free: 433 / Number reflection R work: 7612 / Total number of bins used: 6 / Percent reflection R free: 5.4 / Percent reflection obs: 93.4
Xplor file
Refine IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ATP_XPLOT_PAR.TXT
X-RAY DIFFRACTION3ION_NEUTRALMG.PARAM
X-RAY DIFFRACTION4WATER.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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