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- PDB-1ptd: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C -

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Basic information

Entry
Database: PDB / ID: 1ptd
TitlePHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
ComponentsPHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE (PHOSPHORIC DIESTER) / HYDROLASE / PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C
Function / homology
Function and homology information


phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region
Similarity search - Function
: / 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 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsHeinz, D.W. / Ryan, M. / Bullock, T.L. / Griffith, O.H.
Citation
Journal: EMBO J. / Year: 1995
Title: Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol.
Authors: Heinz, D.W. / Ryan, M. / Bullock, T.L. / Griffith, O.H.
#1: Journal: Biophys.J. / Year: 1993
Title: Crystallization of Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus
Authors: Bullock, T.L. / Ryan, M. / Kim, S.L. / Remington, S.J. / Griffith, O.H.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Phosphatidylinositol-Specific Phospholipase C of Bacillus Cereus: Cloning, Sequencing, and Relationship to Other Phospholipases
Authors: Kuppe, A. / Evans, L.M. / Mcmillen, D.A. / Griffith, O.H.
History
DepositionMay 24, 1995Processing site: BNL
Revision 1.0Jul 11, 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C


Theoretical massNumber of molelcules
Total (without water)34,5691
Polymers34,5691
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 45.600, 160.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C / PI-PLC


Mass: 34568.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: PI-PLC GENE / Plasmid: PBR322 RELATED / Gene (production host): PI-PLC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P14262, EC: 3.1.4.10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.4 Å3/Da / Density % sol: 45 %

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11300 / % possible obs: 88 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
SDMSdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.6→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.264 --
Rwork0.187 --
obs0.187 9528 86 %
Displacement parametersBiso mean: 19.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 0 52 3043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.05
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

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