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- PDB-1aod: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM LISTERIA MONOC... -

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Basic information

Entry
Database: PDB / ID: 1aod
TitlePHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C FROM LISTERIA MONOCYTOGENES
ComponentsPHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE / PHOSPHOLIPID DEGRADATION / VIRULENCE FACTOR OF HUMAN PATHOGEN
Function / homology
Function and homology information


phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region / cytoplasm
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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHeinz, D.W. / Moser, J.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes.
Authors: Moser, J. / Gerstel, B. / Meyer, J.E. / Chakraborty, T. / Wehland, J. / Heinz, D.W.
History
DepositionJul 2, 1997Processing site: BNL
Revision 1.0Jan 7, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1532
Polymers32,9731
Non-polymers1801
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.100, 82.100, 92.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 32972.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOUND MYO-INOSITOL IN ACTIVE SITE / Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD SEROTYPE 1/2A / Cell line: BL21 / Cellular location: SECRETED INTO MEDIUM / Gene: PLCA / Plasmid: PLCA / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): PLCA DELETION VARIANT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P34024, EC: 3.1.4.10
#2: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5
Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.1 M NA-HEPES PH 7.5, 0.8 M NA-K-TARTRATE, 45 MM MYO-INOSITOL
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16.5 mg/mlprotein1drop
30.1 MNa-Hepes1reservoir
40.8 MNa/K-tartrate1reservoir
2precipitant1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 1996 / Details: MIRROR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→24 Å / Num. obs: 10914 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.104 / Net I/σ(I): 7.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.41 / % possible all: 97
Reflection
*PLUS
% possible obs: 95.3 % / Num. measured all: 43095 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PTD

1ptd


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.0065 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001
Isotropic thermal model: GROUPED B-FACTOR REFINEME 2 PARAMETERS PER RESIDUE
Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1108 10.3 %RANDOM
Rwork0.158 ---
obs0.158 10774 94.4 %-
Displacement parametersBiso mean: 31.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-20 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 12 94 2314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.11
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: 2.6→2.72 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.248 88 6.24 %
Rwork0.241 808 -
obs--63.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOP19X.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3INO.PARINO.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.11
LS refinement shell
*PLUS
Rfactor obs: 0.241

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