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

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Basic information

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


positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of norepinephrine secretion / phosphoinositide phospholipase C / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / response to aluminum ion / phosphatidylinositol metabolic process / inositol 1,4,5 trisphosphate binding / phosphatidylinositol-4,5-bisphosphate phospholipase C activity ...positive regulation of inositol trisphosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / response to prostaglandin F / positive regulation of norepinephrine secretion / phosphoinositide phospholipase C / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / response to aluminum ion / phosphatidylinositol metabolic process / inositol 1,4,5 trisphosphate binding / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / 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 / mitochondrial membrane / phospholipid binding / response to peptide hormone / response to calcium ion / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / angiogenesis / intracellular signal transduction / G protein-coupled receptor signaling pathway / calcium ion binding / enzyme binding / plasma membrane / cytosol / cytoplasm
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 / 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 / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Pleckstrin homology 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 (PI) phosphodiesterase / 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 / 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_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.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

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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)142,09110
Polymers141,1492
Non-polymers9428
Water13,367742
1
A: PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0465
Polymers70,5751
Non-polymers4714
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)71,0465
Polymers70,5751
Non-polymers4714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)398.250, 398.250, 398.250
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(0.649075, -0.007093, 0.760691), (0.096938, 0.992576, -0.073459), (-0.754523, 0.121421, 0.644944)91.325, -10.754, 90.71
2given(0.641512, -0.039846, 0.766077), (0.096214, 0.994943, -0.028819), (-0.761055, 0.092195, 0.642102)92.706, -9.1256, 91.1172
3given(0.643425, -0.022884, 0.765167), (0.078093, 0.9963, -0.035872), (-0.761516, 0.082835, 0.642831)91.9101, -7.9031, 91.5277

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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 BARIUM
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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ba
#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.: 742 / 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: 4.66 Å3/Da / Density % sol: 73.6 %
Crystal growpH: 5.2 / Details: pH 5.2
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 12, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 92551 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 35 Å / Num. measured all: 384574
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.271

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Processing

Software
NameVersionClassification
TNT5Erefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.5→10 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3899 4 %SHELLS
Rwork0.21 ---
all-88488 --
obs-88488 --
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8502 0 13 742 9257
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01587051
X-RAY DIFFRACTIONt_angle_deg1.43117261.2
X-RAY DIFFRACTIONt_dihedral_angle_d18.5951740
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0182281
X-RAY DIFFRACTIONt_gen_planes0.01512625
X-RAY DIFFRACTIONt_it2.4387055
X-RAY DIFFRACTIONt_nbd0.04327020
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0181
X-RAY DIFFRACTIONt_plane_restr0.0155

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