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- PDB-4s3g: Structure of the F249X mutant of Phosphatidylinositol-specific ph... -

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Basic information

Entry
Database: PDB / ID: 4s3g
TitleStructure of the F249X mutant of Phosphatidylinositol-specific phospholipase C from Staphylococcus aureus
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / TIM barrel / cation-pi / phospholipase
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 X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus str. Newman (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHe, T. / Gershenson, A. / Eyles, S.J. / Gao, J. / Roberts, M.F.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Fluorinated Aromatic Amino Acids Distinguish Cation-pi Interactions from Membrane Insertion.
Authors: He, T. / Gershenson, A. / Eyles, S.J. / Lee, Y.J. / Liu, W.R. / Wang, J. / Gao, J. / Roberts, M.F.
History
DepositionJan 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5003
Polymers34,2611
Non-polymers2392
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.050, 60.050, 191.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 34260.949 Da / Num. of mol.: 1 / Fragment: UNP residues 11-312 / Mutation: F249X (X=PF5)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus str. Newman (bacteria)
Strain: Newman / Gene: plc / Production host: Escherichia coli (E. coli)
References: UniProt: P45723, phosphatidylinositol diacylglycerol-lyase
#2: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Comment: neurotransmitter, hormone*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 22% PEG 4000, 0.15 M ammonium acetate, 0.1 M sodium acetate, 0.01M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K, temperature 277.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 30, 2014
RadiationMonochromator: Rigaku Micromax-07 HF microfocus / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→42.26 Å / Num. all: 12856 / Num. obs: 12823 / % possible obs: 99.7 % / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.73 % / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.26 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 33.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 623 4.86 %Random
Rwork0.2118 ---
obs0.2155 12821 99.68 %-
all-12862 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 16 54 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012480
X-RAY DIFFRACTIONf_angle_d1.3373356
X-RAY DIFFRACTIONf_dihedral_angle_d15.063895
X-RAY DIFFRACTIONf_chiral_restr0.06356
X-RAY DIFFRACTIONf_plane_restr0.005427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.75160.44111480.31782978X-RAY DIFFRACTION100
2.7516-3.14970.42971670.29172962X-RAY DIFFRACTION100
3.1497-3.96780.27471490.21633047X-RAY DIFFRACTION100
3.9678-42.260.22911590.16943211X-RAY DIFFRACTION99

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