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- PDB-1dji: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1dji
TitlePHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH CALCIUM
ComponentsPHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
KeywordsLIPID DEGRADATION / PHOSPHORIC DIESTER HYDROLASE / HYDROLASE / TRANSDUCER / CALCIUM-BINDING / PHOSPHOLIPASE C / PHOSPHOINOSITIDE-SPECIFIC
Function / homology
Function and homology information


phospholipase C/protein kinase C signal transduction / positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / phosphoinositide phospholipase C / response to aluminum ion / positive regulation of norepinephrine secretion / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol-4,5-bisphosphate phospholipase C activity ...phospholipase C/protein kinase C signal transduction / positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / phosphoinositide phospholipase C / response to aluminum ion / positive regulation of norepinephrine secretion / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol metabolic process / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / GTPase activating protein binding / labyrinthine layer blood vessel development / response to hyperoxia / lipid catabolic process / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / response to peptide hormone / response to calcium ion / mitochondrial membrane / phospholipid binding / regulation of cell population proliferation / angiogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / G protein-coupled receptor signaling pathway / calcium ion binding / enzyme binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Pleckstrin homology domain / Phosphatidylinositol (PI) phosphodiesterase / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Pleckstrin homology domain / Phosphatidylinositol (PI) phosphodiesterase / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / EF-hand / Recoverin; domain 1 / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsEssen, L.-O. / Perisic, O. / Williams, R.L.
CitationJournal: Biochemistry / Year: 1997
Title: A ternary metal binding site in the C2 domain of phosphoinositide-specific phospholipase C-delta1.
Authors: Essen, L.O. / Perisic, O. / Lynch, D.E. / Katan, M. / Williams, R.L.
History
DepositionSep 25, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
B: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,50810
Polymers141,1492
Non-polymers3598
Water15,745874
1
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7545
Polymers70,5751
Non-polymers1794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7545
Polymers70,5751
Non-polymers1794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)398.030, 398.030, 398.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.64751, -0.001367, 0.761255), (0.106663, 0.990392, -0.088018), (-0.753811, 0.138368, 0.642358)91.108, -12.013, 90.097
2given(0.63534, -0.03776, 0.771309), (0.098664, 0.994587, -0.032581), (-0.765904, 0.096801, 0.635626)92.9995, -9.4098, 91.0356
3given(0.640179, -0.023328, 0.767871), (0.086272, 0.995399, -0.041685), (-0.763366, 0.092932, 0.639246)91.9814, -8.6783, 91.1369

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Components

#1: Protein PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1 / PLC-D1


Mass: 70574.516 Da / Num. of mol.: 2 / Mutation: DELTA(1-132) DELETION VARIANT
Source method: isolated from a genetically manipulated source
Details: CATALYTICALLY-ACTIVE DELETION VARIANT THAT LACKS AN N-TERMINAL PH DOMAIN, COMPLEXED WITH CALCIUM
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: CDNA FRAGMENT / Plasmid: PGEX (PHARMACIA) / Gene (production host): CDNA FRAGMENT / Production host: Escherichia coli (E. coli)
References: UniProt: P10688, phosphoinositide phospholipase C
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 874 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.65 Å3/Da / Density % sol: 73.56 %
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Essen, L.O., (1996) Nature, 380, 595.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 Mammonium phosphate1reservoir
25 mg/mlprotein1drop
35 mMTris-HCl1drop
450 mM1dropNaCl
50.25 mMEGTA1drop
60.5 mMDTT1drop
70.005 %(w/v)sodium azide1drop
80.05 %(w/v)CHAPSO1drop
90.7 Mammonium phosphate1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 90470 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 34 Å / Num. measured all: 397693
Reflection shell
*PLUS
% possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.296

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 2.5→10 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3908 4 %SHELLS
Rwork0.22 ---
obs-86499 98 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8515 0 14 874 9403
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01387191
X-RAY DIFFRACTIONt_angle_deg1.3117451.2
X-RAY DIFFRACTIONt_dihedral_angle_d18.0351830
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0132301
X-RAY DIFFRACTIONt_gen_planes0.01412635
X-RAY DIFFRACTIONt_it2.487195
X-RAY DIFFRACTIONt_nbd0.01426520
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0131
X-RAY DIFFRACTIONt_plane_restr0.0145

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