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- PDB-4ptd: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C MUTANT D274N -

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Basic information

Entry
Database: PDB / ID: 4ptd
TitlePHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C MUTANT D274N
ComponentsPHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE / PHOSPHORIC DIESTER / LIPID DEGRADATION / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHeinz, D.W.
Citation
Journal: Biochemistry / Year: 1997
Title: Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis.
Authors: Gassler, C.S. / Ryan, M. / Liu, T. / Griffith, O.H. / Heinz, D.W.
#1: 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.
History
DepositionJul 18, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 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: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C


Theoretical massNumber of molelcules
Total (without water)34,5681
Polymers34,5681
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.700, 44.600, 153.300
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: 34567.680 Da / Num. of mol.: 1 / Mutation: D274N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Description: GENE CLONED IN ESCHERICHIA COLI / Cellular location: SECRETED INTO MEDIUM / Gene: PI-PLC GENE / Plasmid: PBR322 RELATED / Cellular location (production host): PERIPLASM / Gene (production host): PI-PLC D198E GENE / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 / References: UniProt: P14262, EC: 3.1.4.10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 mg/mlprotein1drop
218 mMHEPES1drop
30.0045 %1dropNaN3
416.36 %PEG6001drop
50.09 Mtrisodium citrate1drop
66.45 mM1dropCdCl2
71.5-2.25 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Nov 25, 1996 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→6.3 Å / Num. obs: 13525 / % possible obs: 86.6 % / Observed criterion σ(I): 0 / Redundancy: 1.57 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.182 / % possible all: 80.9
Reflection
*PLUS
Num. obs: 12218 / Num. measured all: 21317
Reflection shell
*PLUS
% possible obs: 71.3 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE PI-PLC

Resolution: 2.3→6.3 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 584 4 %RANDOM
Rwork0.203 ---
obs0.203 12216 86.6 %-
Displacement parametersBiso mean: 33.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→6.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 0 60 2482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.39
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
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: 2.3→2.4 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.394 64 3.66 %
Rwork0.314 1312 -
obs--78.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
LS refinement shell
*PLUS
Rfactor obs: 0.314

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