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- PDB-5to4: Phospholipase C gamma-1 C-terminal SH2 domain, spacegroup P212121 -

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Basic information

Entry
Database: PDB / ID: 5to4
TitlePhospholipase C gamma-1 C-terminal SH2 domain, spacegroup P212121
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / SH2 / Phospholipase
Function / homology
Function and homology information


calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / COP9 signalosome / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phospholipid catabolic process / phosphatidylinositol-mediated signaling / positive regulation of epithelial cell migration / cellular response to vascular endothelial growth factor stimulus / ruffle ...calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / COP9 signalosome / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phospholipid catabolic process / phosphatidylinositol-mediated signaling / positive regulation of epithelial cell migration / cellular response to vascular endothelial growth factor stimulus / ruffle / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / guanyl-nucleotide exchange factor activity / ruffle membrane / epidermal growth factor receptor signaling pathway / lamellipodium / in utero embryonic development / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / PLCG EF-hand motif 2 / 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 C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / SH2 domain / SHC Adaptor Protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsWuttke, D.S. / McKercher, M.A.
CitationJournal: Biochemistry / Year: 2017
Title: Multimodal Recognition of Diverse Peptides by the C-Terminal SH2 Domain of Phospholipase C-gamma 1 Protein.
Authors: McKercher, M.A. / Guan, X. / Tan, Z. / Wuttke, D.S.
History
DepositionOct 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9901
Polymers11,9901
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.030, 36.440, 88.380
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 gamma-1 / PLC-148 / Phosphoinositide phospholipase C-gamma-1 / Phospholipase C-II / PLC-II / Phospholipase C- ...PLC-148 / Phosphoinositide phospholipase C-gamma-1 / Phospholipase C-II / PLC-II / Phospholipase C-gamma-1 / PLC-gamma-1


Mass: 11989.685 Da / Num. of mol.: 1 / Fragment: UNP residues 663-759
Source method: isolated from a genetically manipulated source
Details: Scattered electron density was also present for at least two additional polymers, likely low molecular weight polyethylene glycol molecules. However, the molecules could not be fit into the ...Details: Scattered electron density was also present for at least two additional polymers, likely low molecular weight polyethylene glycol molecules. However, the molecules could not be fit into the density non-ambiguously and were consequently omitted from the model.
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: PLCG1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P08487, phosphoinositide phospholipase C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate (pH 5.5), 22% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.44 Å / Num. all: 12342 / Num. obs: 12342 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.08 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Rsym value: 0.084 / Net I/av σ(I): 4.706 / Net I/σ(I): 12.8 / Num. measured all: 80381
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.796.60.2672.4197.7
1.79-1.96.80.1953.5197.8
1.9-2.036.80.1414.7198.1
2.03-2.196.80.1145.7197.8
2.19-2.46.60.1016.2198.2
2.4-2.696.40.0847.5198.9
2.69-3.16.30.0778198.9
3.1-3.85.70.0847198.7
3.8-5.386.10.0678.9198.6
5.38-36.4460.05910.4188.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å36.44 Å
Translation1.7 Å36.44 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K44

4k44


Resolution: 1.7→28.114 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.2211 614 5 %
Rwork0.1837 --
obs0.1855 12291 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.19 Å2 / Biso mean: 29.6369 Å2 / Biso min: 10.26 Å2
Refinement stepCycle: final / Resolution: 1.7→28.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 80 907
Biso mean---34.48 -
Num. residues----99
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01885
X-RAY DIFFRACTIONf_angle_d1.0211195
X-RAY DIFFRACTIONf_chiral_restr0.054119
X-RAY DIFFRACTIONf_plane_restr0.006157
X-RAY DIFFRACTIONf_dihedral_angle_d17.411545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.87110.25521520.20642847299997
1.8711-2.14180.2551500.18582879302997
2.1418-2.6980.22251550.1932914306998
2.698-28.11790.20581570.17513037319496

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