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- PDB-2zkm: Crystal Structure of Phospholipase C Beta 2 -

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Basic information

Entry
Database: PDB / ID: 2zkm
TitleCrystal Structure of Phospholipase C Beta 2
Components1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2
KeywordsHYDROLASE / phospholipase C / phosphoinositide phospholipase / PLC-Beta-2 / Calcium / Coiled coil / Lipid degradation / Metal-binding / Transducer
Function / homology
Function and homology information


G-protein beta/gamma-subunit complex / phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / detection of chemical stimulus involved in sensory perception of bitter taste / phosphatidylinositol metabolic process / PLC beta mediated events / phosphatidylinositol phospholipase C activity / phospholipase C activity / phosphatidylinositol-mediated signaling ...G-protein beta/gamma-subunit complex / phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / detection of chemical stimulus involved in sensory perception of bitter taste / phosphatidylinositol metabolic process / PLC beta mediated events / phosphatidylinositol phospholipase C activity / phospholipase C activity / phosphatidylinositol-mediated signaling / neuronal dense core vesicle / Synthesis of IP3 and IP4 in the cytosol / activation of phospholipase C activity / phospholipid metabolic process / lipid catabolic process / release of sequestered calcium ion into cytosol / phospholipid binding / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / G protein-coupled receptor signaling pathway / calcium ion binding / cytosol
Similarity search - Function
: / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2 / PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain ...: / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2 / PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol (PI) phosphodiesterase / Phosphatidylinositol-specific phospholipase X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PH-domain like / EF-hand / Recoverin; domain 1 / C2 domain superfamily / EF-hand domain pair / Roll / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.62 Å
AuthorsHicks, S.N. / Jezyk, M.R. / Gershberg, S. / Seifert, J.P. / Harden, T.K. / Sondek, J.
Citation
Journal: Mol.Cell / Year: 2008
Title: General and versatile autoinhibition of PLC isozymes
Authors: Hicks, S.N. / Jezyk, M.R. / Gershburg, S. / Seifert, J.P. / Harden, T.K. / Sondek, J.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Crystal structure of Rac1 bound to its effector phospholipase C-beta2
Authors: Jezyk, M.R. / Snyder, J.T. / Gershberg, S. / Worthylake, D.K. / Harden, T.K. / Sondek, J.
History
DepositionMar 26, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0742
Polymers91,0341
Non-polymers401
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.404, 86.379, 147.447
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta-2 / Phosphoinositide phospholipase C / Phospholipase C- beta-2 / PLC-beta-2


Mass: 91033.922 Da / Num. of mol.: 1 / Fragment: residues 1-799 (PH-C2 domains)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLC beta 2 / Plasmid: pFastBacHT C / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q00722, phosphoinositide phospholipase C
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16%(v/v) isopropanol, 2%(v/v) dioxane, 100mM Tris , pH 8.5, VAPOR DIFFUSION, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0712 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2004
RadiationMonochromator: double crystal Si (220) cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. all: 130702 / Num. obs: 129374 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.065 / Χ2: 0.867 / Net I/σ(I): 12.2
Reflection shellResolution: 1.62→1.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.207 / Num. unique all: 12374 / Χ2: 0.613 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å37.27 Å
Translation2.5 Å37.27 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FJU

2fju


Resolution: 1.62→19.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.235 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 6470 5 %RANDOM
Rwork0.196 ---
obs0.197 129234 98.88 %-
all-130702 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.682 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.62→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 1 692 6397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225843
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.9697894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28924.361266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.155151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9151529
X-RAY DIFFRACTIONr_chiral_restr0.0680.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024392
X-RAY DIFFRACTIONr_nbd_refined0.180.22673
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2569
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.217
X-RAY DIFFRACTIONr_mcbond_it0.5091.53662
X-RAY DIFFRACTIONr_mcangle_it0.84525770
X-RAY DIFFRACTIONr_scbond_it1.29532471
X-RAY DIFFRACTIONr_scangle_it1.9864.52124
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 466 -
Rwork0.213 8605 -
all-9071 -
obs--95.01 %

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