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- PDB-6irc: C-terminal domain of Drosophila phospholipase b NORPA, methylated -

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Basic information

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


PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / G alpha (q) signalling events / : / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / negative regulation of opsin-mediated signaling pathway / 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 / : / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / negative regulation of opsin-mediated signaling pathway / 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 / thermotaxis / phosphatidylinositol phospholipase C activity / phospholipase C activity / photoreceptor cell maintenance / phosphatidylinositol-mediated signaling / entrainment of circadian clock by photoperiod / 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: 3.538 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,5341
Polymers27,5341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.209, 119.209, 116.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 27533.676 Da / Num. of mol.: 1
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

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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: 4.34 Å3/Da / Density % sol: 71.63 %
Crystal growTemperature: 289 K / Method: liquid diffusion / Details: 3.8M Sodium Formate, 100mM Bis-tris Propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 5961 / % possible obs: 94.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 89.66 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.04 / Rrim(I) all: 0.133 / Χ2: 2.08 / Net I/σ(I): 8.2 / Num. measured all: 68157
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.5611.40.6123000.7020.2030.6481.70294.9
3.56-3.6311.50.3922750.8730.130.4152.05996.5
3.63-3.6911.10.3243000.8890.1110.3452.01796.2
3.69-3.7711.40.2982910.8810.10.3171.9395.7
3.77-3.8511.80.2412920.9780.0760.2541.79195.7
3.85-3.9411.50.243010.9580.0770.2541.98595.9
3.94-4.0411.90.2382850.9560.0750.2511.95895.6
4.04-4.1511.40.2322910.9690.0740.2451.9995.4
4.15-4.2711.60.1532970.980.0480.1622.06195.5
4.27-4.4111.50.1372950.990.0420.1442.17494.6
4.41-4.5711.60.1472970.990.0440.1542.20894.9
4.57-4.7511.80.1492900.9910.0450.1572.3394.5
4.75-4.9711.80.1263050.9940.0370.1322.21395.3
4.97-5.23120.1312880.9950.0380.1371.96794.4
5.23-5.5511.80.1513030.9930.0440.1581.8494.7
5.55-5.9811.70.1733000.9860.0510.1811.82994
5.98-6.5811.70.1363040.9940.040.1431.90793.8
6.58-7.5311.40.1153050.9960.0350.1212.18593.3
7.53-9.4811.10.063110.9980.0180.0632.44692
9.48-509.20.0513310.9980.0170.0543.14387.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 3.538→30.957 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 319 5.38 %
Rwork0.2442 --
obs0.2467 5933 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.62 Å2 / Biso mean: 103.7332 Å2 / Biso min: 54.46 Å2
Refinement stepCycle: final / Resolution: 3.538→30.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1521 0 0 0 1521
Num. residues----211
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.2201-5.7252-1.59174.6075-1.32056.5778-0.42420.29291.416-1.71920.3417-0.72040.2091-0.8515-0.11980.74680.0177-0.17760.6206-0.25190.941370.3756.42120.98
24.9027-3.40462.31846.5848-3.49324.13090.67570.1482-0.0399-1.5501-0.65960.00320.6439-0.1603-0.12510.82060.01180.02920.6712-0.08540.697885.64229.5488121.9021
39.6051-5.6371-5.42174.07744.41445.0125-0.67370.4394-2.01531.2534-1.8217-1.6666-1.02391.7885-1.23021.24680.2179-0.35271.00310.4481.2479109.20818.9879133.3322
410.0362-6.38033.59088.6472-4.03863.42090.42630.24850.6371-0.9072-0.4065-0.70940.31360.10570.27320.93230.05470.03720.56-0.00151.220392.156537.2628120.9892
54.9752-0.0830.88984.17231.21791.06620.1788-2.2604-1.18390.0730.11291.7253-0.0782-0.2943-0.25150.95760.10110.0640.99260.06641.357344.643277.663115.1854
66.591-5.6289-2.25735.00741.9590.6991-1.2025-2.16943.33050.53490.5392-0.787-0.1589-0.05130.75940.85820.0302-0.4310.9297-0.2521.752341.568692.1602112.8504
78.8972-2.85240.88675.2529-0.71371.02530.25431.1627-1.2521-1.0547-0.51591.07940.59150.03590.3120.84380.0952-0.12370.72050.09450.860776.457663.5849116.346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 865 through 879 )A865 - 879
2X-RAY DIFFRACTION2chain 'A' and (resid 880 through 912 )A880 - 912
3X-RAY DIFFRACTION3chain 'A' and (resid 913 through 930 )A913 - 930
4X-RAY DIFFRACTION4chain 'A' and (resid 931 through 978 )A931 - 978
5X-RAY DIFFRACTION5chain 'A' and (resid 979 through 1019 )A979 - 1019
6X-RAY DIFFRACTION6chain 'A' and (resid 1020 through 1044 )A1020 - 1044
7X-RAY DIFFRACTION7chain 'A' and (resid 1045 through 1080 )A1045 - 1080

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