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- PDB-5tnw: Phospholipase C gamma-1 C-terminal SH2 domain -

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Basic information

Entry
Database: PDB / ID: 5tnw
TitlePhospholipase C gamma-1 C-terminal SH2 domain
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 / phospholipid catabolic process / phosphatidylinositol metabolic process / COP9 signalosome / phosphatidylinositol phospholipase C activity / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to vascular endothelial growth factor stimulus / release of sequestered calcium ion into cytosol ...calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / phospholipid catabolic process / phosphatidylinositol metabolic process / COP9 signalosome / phosphatidylinositol phospholipase C activity / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to vascular endothelial growth factor stimulus / release of sequestered calcium ion into cytosol / ruffle / cellular response to epidermal growth factor stimulus / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / ruffle membrane / lamellipodium / in utero embryonic development / calcium ion binding / plasma membrane / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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 ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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 / EF-Hand 1, calcium-binding site / SH2 domain superfamily / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsWuttke, D.S. / McKercher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1121842 United States
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 14, 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 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)23,9792
Polymers23,9792
Non-polymers00
Water4,738263
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)11,9901
Polymers11,9901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)11,9901
Polymers11,9901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.360, 36.650, 38.780
Angle α, β, γ (deg.)90.200, 101.890, 97.200
Int Tables number1
Space group name H-MP1

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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.: 2 / Fragment: UNP residues 663-759
Source method: isolated from a genetically manipulated source
Details: Electron density suggests a modification to the side chain of cysteine 715 in both chains A and B. The chemical composition of the modification was unclear, and was consequently left out of the final model.
Source: (gene. exp.) Bos taurus (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.: 263 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Imidazole (pH 7.0), 20% Jeffamine ED-2001 (pH 7.0)

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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: 1.366→37.931 Å / Num. all: 34467 / Num. obs: 34467 / % possible obs: 91.2 % / Redundancy: 2 % / Biso Wilson estimate: 11.84 Å2 / Rpim(I) all: 0.069 / Rrim(I) all: 0.105 / Rsym value: 0.078 / Net I/av σ(I): 4.833 / Net I/σ(I): 5.7 / Num. measured all: 68865
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.37-1.441.70.2722.4184.1
1.44-1.5320.193.5190.9
1.53-1.632.10.1434.4192
1.63-1.762.10.125.1192.2
1.76-1.932.10.1045.7192.8
1.93-2.162.10.087.5193.4
2.16-2.4920.0757.8193.6
2.49-3.051.90.0718.4192.4
3.05-4.3220.0698.1194.9
4.32-37.93120.04911.5188.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.05 Å37.93 Å
Translation4.05 Å37.93 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: 1.4→37.931 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.215 1622 5.02 %
Rwork0.187 --
obs0.1884 32335 92.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.53 Å2 / Biso mean: 18.5711 Å2 / Biso min: 5.11 Å2
Refinement stepCycle: final / Resolution: 1.4→37.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 0 285 1947
Biso mean---26.28 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041716
X-RAY DIFFRACTIONf_angle_d0.7222304
X-RAY DIFFRACTIONf_chiral_restr0.067231
X-RAY DIFFRACTIONf_plane_restr0.004299
X-RAY DIFFRACTIONf_dihedral_angle_d16.232668
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.44120.27561250.25252488261389
1.4412-1.48770.26331420.23092492263491
1.4877-1.54090.26031290.21712554268391
1.5409-1.60260.23461540.2032543269792
1.6026-1.67550.22011250.19752550267592
1.6755-1.76390.23221310.18712583271492
1.7639-1.87440.19391290.18342591272093
1.8744-2.01910.21411460.192571271793
2.0191-2.22230.21061410.17922613275494
2.2223-2.54380.2651400.19012588272893
2.5438-3.20460.19011270.18312572269993
3.2046-37.94460.1811330.16942568270192

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