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

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Basic information

Entry
Database: PDB / ID: 1djg
TitlePHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH LANTHANUM
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


Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of inositol trisphosphate biosynthetic process / phosphatidylinositol phosphate binding / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol metabolic process / response to aluminum ion / phosphatidylinositol phospholipase C activity / phosphatidic acid binding ...Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of inositol trisphosphate biosynthetic process / phosphatidylinositol phosphate binding / phosphoinositide phospholipase C / positive regulation of norepinephrine secretion / phosphatidylinositol metabolic process / response to aluminum ion / phosphatidylinositol phospholipase C activity / phosphatidic acid binding / phospholipase C activity / inositol 1,4,5 trisphosphate binding / calcium-dependent phospholipid binding / phosphatidylinositol-mediated signaling / GTPase activating protein binding / labyrinthine layer blood vessel development / response to hyperoxia / lipid catabolic process / release of sequestered calcium ion into cytosol / response to organonitrogen compound / phosphatidylinositol-4,5-bisphosphate binding / regulation of cytosolic calcium ion concentration / mitochondrial membrane / phospholipid binding / response to peptide hormone / response to calcium ion / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / angiogenesis / G protein-coupled receptor signaling pathway / calcium ion binding / enzyme binding / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Pleckstrin homology domain / 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 ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 / : / Pleckstrin homology domain / 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 (PI) phosphodiesterase / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / LANTHANUM (III) ION / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 1.3Jun 27, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)142,37812
Polymers141,1492
Non-polymers1,22910
Water12,755708
1
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1896
Polymers70,5751
Non-polymers6155
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)71,1896
Polymers70,5751
Non-polymers6155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)397.920, 397.920, 397.920
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(0.657608, -0.009698, 0.753298), (0.098559, 0.992431, -0.073262), (-0.746886, 0.122422, 0.653586)90.078, -10.519, 90.31
2given(0.646684, -0.041248, 0.761642), (0.092036, 0.995461, -0.024235), (-0.757185, 0.085771, 0.647545)91.7698, -8.2721, 91.109
3given(0.650942, -0.026581, 0.758662), (0.076892, 0.996556, -0.031058), (-0.755223, 0.078552, 0.650744)90.8218, -7.2061, 91.345

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Components

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


Mass: 70574.516 Da / Num. of mol.: 2 / Mutation: DEL(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 LANTHANUM
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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-LA / LANTHANUM (III) ION / Lanthanum


Mass: 138.905 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: La
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 70 %
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: ESRF / Beamline: ID2 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 4, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionNum. obs: 81095 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 53 Å / Num. measured all: 384052
Reflection shell
*PLUS
% possible obs: 90.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.17

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Processing

Software
NameVersionClassification
TNT5Erefinement
MOSFLMdata reduction
RefinementResolution: 2.6→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.27 3297 4 %
Rwork0.21 --
all-77696 -
obs-77696 98.5 %
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8522 0 16 708 9246
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01687231
X-RAY DIFFRACTIONt_angle_deg1.41117501.2
X-RAY DIFFRACTIONt_dihedral_angle_d18.2851860
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0162291
X-RAY DIFFRACTIONt_gen_planes0.0162291
X-RAY DIFFRACTIONt_it2.6465
X-RAY DIFFRACTIONt_nbd0.06330120
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0161
X-RAY DIFFRACTIONt_plane_restr0.0161

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