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- PDB-6irb: C-terminal coiled coil domain of Drosophila phospholipase C beta ... -

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Basic information

Entry
Database: PDB / ID: 6irb
TitleC-terminal coiled coil domain of Drosophila phospholipase C beta NORPA, selenomethionine
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
KeywordsHYDROLASE / phospholipase C beta / coiled coil / drosophila selenomethionine
Function / homology
Function and homology information


PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / G alpha (q) signalling events / light-induced release of internally sequestered calcium ion / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / deactivation of rhodopsin mediated signaling / rhabdomere / positive regulation of clathrin-dependent endocytosis / mucosal immune response ...PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / G alpha (q) signalling events / light-induced release of internally sequestered calcium ion / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / deactivation of rhodopsin mediated signaling / rhabdomere / positive regulation of clathrin-dependent endocytosis / mucosal immune response / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / detection of chemical stimulus involved in sensory perception of bitter taste / rhodopsin mediated signaling pathway / cellular response to light stimulus / phosphatidylinositol metabolic process / phospholipid biosynthetic process / entrainment of circadian clock / phosphatidylinositol phospholipase C activity / thermotaxis / phospholipase C activity / photoreceptor cell maintenance / entrainment of circadian clock by photoperiod / phosphatidylinositol-mediated signaling / phototransduction / phospholipid metabolic process / lipid catabolic process / release of sequestered calcium ion into cytosol / visual perception / adult locomotory behavior / calcium-mediated signaling / circadian rhythm / phospholipase C-activating G protein-coupled receptor signaling pathway / calcium ion binding
Similarity search - Function
Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / 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 ...Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / 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-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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / EF-hand domain pair
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.661 Å
AuthorsYe, F. / Li, J. / Huang, Y. / Liu, W. / Zhang, M.
CitationJournal: Elife / Year: 2018
Title: An unexpected INAD PDZ tandem-mediated plc beta binding in Drosophila photo receptors.
Authors: Ye, F. / Huang, Y. / Li, J. / Ma, Y. / Xie, C. / Liu, Z. / Deng, X. / Wan, J. / Xue, T. / Liu, W. / Zhang, M.
History
DepositionNov 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 28, 2020Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)50,1812
Polymers50,1812
Non-polymers00
Water724
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)25,0911
Polymers25,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)25,0911
Polymers25,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.958, 37.591, 140.130
Angle α, β, γ (deg.)90.720, 89.860, 119.440
Int Tables number1
Space group name H-MP1

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase / 1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase beta / No receptor potential A protein ...1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase beta / No receptor potential A protein / Phosphoinositide phospholipase C / Phosphoinositide phospholipase C-beta


Mass: 25090.617 Da / Num. of mol.: 2 / Mutation: K884E,K898E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: norpA, PLC-beta, CG3620 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P13217, phosphoinositide phospholipase C
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 289 K / Method: liquid diffusion / pH: 7.2
Details: 64% 2-Methyl-2,4-pentanediol (MPD), 100mM HEPES, 8% Pentaerythritol ethoxylate (3/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 2.7→50 Å / Num. obs: 17843 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 58.67 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.058 / Rrim(I) all: 0.108 / Χ2: 3.347 / Net I/σ(I): 10.6 / Num. measured all: 59839
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.30.8278340.7850.530.9841.4695.4
2.75-2.83.30.6668530.8530.4270.7941.47396.3
2.8-2.853.30.5539390.9330.3530.6581.41896.6
2.85-2.913.30.4679370.9450.3010.5571.44396.5
2.91-2.973.30.3728450.9640.240.4441.58196
2.97-3.043.30.3358700.9750.2170.41.51296.9
3.04-3.123.40.2719580.9810.1720.3211.56296.9
3.12-3.23.30.3038550.9670.1960.3621.63996.3
3.2-3.33.30.2468660.9760.1580.2941.74495.8
3.3-3.43.30.2039320.9780.1290.2411.77996.3
3.4-3.523.30.1278570.9890.0820.1521.9296
3.52-3.663.30.0948740.9930.060.1121.94993.4
3.66-3.833.30.0738670.9960.0470.0882.12789.6
3.83-4.033.40.0668630.9980.0420.0782.2998.7
4.03-4.293.40.0579390.9980.0360.0682.40698.7
4.29-4.623.40.0559030.9970.0350.0662.75598.8
4.62-5.083.40.0569070.9970.0360.0673.10599.1
5.08-5.813.50.0749260.9970.0460.0875.20599.4
5.81-7.323.40.0869360.9940.0540.1028.2799.5
7.32-503.40.0658820.9970.0420.07720.14195.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.661→14.904 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Phase error: 35.18 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2798 918 5.21 %
Rwork0.2246 --
obs0.2276 17606 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.71 Å2 / Biso mean: 94.2019 Å2 / Biso min: 23.88 Å2
Refinement stepCycle: final / Resolution: 2.661→14.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 0 4 3361
Biso mean---34.62 -
Num. residues----418
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.53040.34820.62241.70720.68961.2507-0.140.06660.1112-0.4257-0.26670.1568-0.3171-0.3699-0.07340.5774-0.0580.07220.9517-0.40730.486417.342415.8541-76.9067
2-0.07080.21820.36733.22184.86196.53340.0232-0.09320.0461-0.3029-0.17530.1063-0.6906-0.08680.09551.3764-0.0458-0.01350.9172-0.29940.620216.032220.3652-14.6945
33.145-0.0119-0.06822.44461.98729.1323-0.15370.5288-0.28390.12990.03890.14891.1896-0.04720.1230.5926-0.02190.04210.374-0.09890.462120.5811-27.5097-82.7596
40.0825-0.4617-0.29192.40591.55160.97880.0641-0.25770.06430.0652-0.25120.2014-0.7599-0.1665-0.01191.13570.04160.05030.9881-0.36720.638516.7116-53.1385-181.9571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 85 through 234 )B85 - 234
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 172 )A23 - 172
3X-RAY DIFFRACTION3chain 'A' and (resid 173 through 234 )A173 - 234
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 84 )B23 - 84

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