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- PDB-6s2a: PI PLC mutant H82A -

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Basic information

Entry
Database: PDB / ID: 6s2a
TitlePI PLC mutant H82A
Components1-phosphatidylinositol phosphodiesterase
KeywordsLIPID BINDING PROTEIN / PI PLC / inositol
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
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEisenreichova, A. / Boura, E.
CitationJournal: To Be Published
Title: PI PLC mutant H82A
Authors: Eisenreichova, A. / Boura, E.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol phosphodiesterase
B: 1-phosphatidylinositol phosphodiesterase
C: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9136
Polymers104,3733
Non-polymers5403
Water2,684149
1
A: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9712
Polymers34,7911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9712
Polymers34,7911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9712
Polymers34,7911
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.759, 130.759, 216.898
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein 1-phosphatidylinositol phosphodiesterase / Phosphatidylinositol diacylglycerol-lyase / Phosphatidylinositol-specific phospholipase C / PI-PLC


Mass: 34790.945 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P14262, phosphatidylinositol diacylglycerol-lyase
#2: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: Morpheus screen (Molecular dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→48.91 Å / Num. obs: 30812 / % possible obs: 99.85 % / Redundancy: 16.2 % / Net I/σ(I): 10.95
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 2998

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ptd

7ptd


Resolution: 2.7→48.907 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.91
RfactorNum. reflection% reflection
Rfree0.2448 1539 5 %
Rwork0.2162 --
obs0.2177 30794 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 36 149 7424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057464
X-RAY DIFFRACTIONf_angle_d0.82710134
X-RAY DIFFRACTIONf_dihedral_angle_d15.214422
X-RAY DIFFRACTIONf_chiral_restr0.1381083
X-RAY DIFFRACTIONf_plane_restr0.0041299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.35041370.28632593X-RAY DIFFRACTION99
2.7872-2.88680.33581350.28492583X-RAY DIFFRACTION100
2.8868-3.00230.32951380.28312612X-RAY DIFFRACTION100
3.0023-3.1390.28091370.25822617X-RAY DIFFRACTION100
3.139-3.30440.30261390.25472614X-RAY DIFFRACTION100
3.3044-3.51140.25831380.22722631X-RAY DIFFRACTION100
3.5114-3.78240.2931390.21922647X-RAY DIFFRACTION100
3.7824-4.16290.20661390.18312658X-RAY DIFFRACTION100
4.1629-4.76480.1721410.16362681X-RAY DIFFRACTION100
4.7648-6.00150.20861440.18632723X-RAY DIFFRACTION100
6.0015-48.91470.24211520.22422896X-RAY DIFFRACTION100

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