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- PDB-1qat: 1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA C... -

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Basic information

Entry
Database: PDB / ID: 1qat
Title1-PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE PHOSPHODIESTERASE DELTA COMPLEX WITH SAMARIUM (III) CHLORIDE
ComponentsPHOSPHOLIPASE C DELTA-1
KeywordsHYDROLASE / LIPID DEGRADATION / TRANSDUCER / CALCIUM-BINDING
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 / positive regulation of norepinephrine secretion / phosphoinositide phospholipase C / response to aluminum ion / 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 / positive regulation of norepinephrine secretion / phosphoinositide phospholipase C / response to aluminum ion / 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 / mitochondrial membrane / phospholipid binding / response to peptide hormone / response to calcium ion / 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 / 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
SAMARIUM (III) ION / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å
AuthorsGrobler, J.A. / Hurley, J.H.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: C2 domain conformational changes in phospholipase C-delta 1.
Authors: Grobler, J.A. / Essen, L.O. / Williams, R.L. / Hurley, J.H.
#1: Journal: Nature / Year: 1996
Title: Crystal Structure of a Mammalian Phosphoinositide-Specific Phospholipase C Delta
Authors: Essen, L.O. / Perisic, O. / Cheung, R. / Katan, M. / Williams, R.L.
#2: Journal: Protein Sci. / Year: 1996
Title: Expression, Characterization, and Crystallization of the Catalytic Core of Rat Phosphatidylinositide-Specific Phospholipase C Delta 1
Authors: Grobler, J.A. / Hurley, J.H.
History
DepositionAug 2, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE C DELTA-1
B: PHOSPHOLIPASE C DELTA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,6137
Polymers140,8612
Non-polymers7525
Water00
1
A: PHOSPHOLIPASE C DELTA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7313
Polymers70,4301
Non-polymers3012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHOLIPASE C DELTA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8814
Polymers70,4301
Non-polymers4513
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.600, 75.100, 86.400
Angle α, β, γ (deg.)66.40, 85.60, 89.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PHOSPHOLIPASE C DELTA-1 / PLC-DELTA-1


Mass: 70430.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C DELTA-1 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: SEED / Plasmid: PET / Production host: Escherichia coli (E. coli)
References: UniProt: P10688, phosphoinositide phospholipase C
#2: Chemical
ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Sm

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growMethod: clusters formed by mixing - used as seeds in hanging drop
pH: 6.5
Details: NEEDLE CLUSTERS WERE FORMED BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (22 MG/ML) WITH A WELL SOLUTION CONSISTING OF 0.1 M NA MES (PH 6.0), 0.2 M LICL, 20% GLYCEROL, AND 12-14 % PEG 8000. ...Details: NEEDLE CLUSTERS WERE FORMED BY MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (22 MG/ML) WITH A WELL SOLUTION CONSISTING OF 0.1 M NA MES (PH 6.0), 0.2 M LICL, 20% GLYCEROL, AND 12-14 % PEG 8000. FRAGMENTS OF THE NEEDLE CLUSTERS WERE USED TO SEED HANGING DROPS. THE WELL SOLUTION USED FOR THE SEEDING EXPERIMENTS WAS ADJUSTED TO 0.1M NA MES (PH 6.5), 0.2 M LICL, 20 % GLYCEROL, AND 6-8 % PEG 8000., clusters formed by mixing - used as seeds in hanging drops
PH range: 6.0-6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: used to seeding, Grobler, J.A., (1996) Protein Sci., 5, 680.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MNaMes1reservoir
20.2 M1reservoirLiCl
320 %glycerol1reservoir
46-8 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. obs: 24235 / % possible obs: 84.9 % / Observed criterion σ(I): -2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 7.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.248 / % possible all: 73.8

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: APO TRICLINIC PHOSPHOLIPASE C

Resolution: 3→6 Å / Cross valid method: FREE R
RfactorNum. reflection% reflection
Rfree0.261 1217 5.13 %
Rwork0.194 --
obs0.194 22504 -
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8028 0 5 47 8080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
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
LS refinement shellResolution: 3→3.09 Å /
RfactorNum. reflection
Rfree0.288 104
Rwork0.256 2178
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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