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- PDB-1mai: STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM PHOSPHOLIPASE C ... -

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Basic information

Entry
Database: PDB / ID: 1mai
TitleSTRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM PHOSPHOLIPASE C DELTA IN COMPLEX WITH INOSITOL TRISPHOSPHATE
ComponentsPHOSPHOLIPASE C DELTA-1
KeywordsSIGNAL TRANSDUCTION PROTEIN / PLECKSTRIN / PHOSPHOLIPASE / INOSITOL TRISPHOSPHATE / HYDROLASE
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 / regulation of cytosolic calcium ion concentration / phosphatidylinositol-4,5-bisphosphate binding / 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-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 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsFerguson, K.M. / Lemmon, M.A. / Schlessinger, J. / Sigler, P.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain.
Authors: Ferguson, K.M. / Lemmon, M.A. / Schlessinger, J. / Sigler, P.B.
History
DepositionMay 23, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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 / _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: PHOSPHOLIPASE C DELTA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8662
Polymers15,4461
Non-polymers4201
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.400, 59.400, 80.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PHOSPHOLIPASE C DELTA-1


Mass: 15445.579 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH D-MYO-INOSITOL-1,4,5-TRISPHOSPHATE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET11A / Production host: Escherichia coli (E. coli)
References: UniProt: P10688, phosphoinositide phospholipase C
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.2 mMprotein/ligand complex1drop
212 %PEG200001reservoir
310 %glycerol1reservoir
450 mMNa-citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 11978 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.066 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 3.22 / Rsym value: 0.38 / % possible all: 99.4

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.291 -10 %
Rwork0.205 --
obs0.205 11695 99.5 %
Displacement parametersBiso mean: 27.98 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 24 110 1701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.752
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.42
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.113
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Rfactor all: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.42
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.113

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