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- PDB-4f2t: Modulation of S.aureus Phosphatidylinositol-Specific Phospholipas... -

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Basic information

Entry
Database: PDB / ID: 4f2t
TitleModulation of S.aureus Phosphatidylinositol-Specific Phospholipase C Membrane Binding.
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / alpha beta barrel / phosphatidylinostol-specific phospholipase C / membrane interface
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
ACETATE ION / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCheng, J. / Goldstein, R. / Stec, B. / Gershenson, A. / Roberts, M.F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Competition between Anion Binding and Dimerization Modulates Staphylococcus aureus Phosphatidylinositol-specific Phospholipase C Enzymatic Activity.
Authors: Cheng, J. / Goldstein, R. / Stec, B. / Gershenson, A. / Roberts, M.F.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3434
Polymers35,1661
Non-polymers1773
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.088, 55.957, 61.681
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 1-phosphatidylinositol phosphodiesterase / Phosphatidylinositol diacylglycerol-lyase / Phosphatidylinositol-specific phospholipase C / PI-PLC


Mass: 35166.047 Da / Num. of mol.: 1 / Fragment: UNP residues 11-312 / Mutation: Y253S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Gene: plc, NWMN_0041 / Production host: Escherichia coli (E. coli)
References: UniProt: P45723, phosphatidylinositol diacylglycerol-lyase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 16% PEG 4000, 0.150 M ammonium acetate, 0.100 M sodium acetate, 0.100 M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 24, 2012 / Details: Osmic VariMax
RadiationMonochromator: Osmic VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 274181 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.063
Reflection shellResolution: 2→2.03 Å / Redundancy: 12.3 % / Num. unique all: 997 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phaser)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(phaser)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V18

3v18


Resolution: 2.3→29.855 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 678 5.01 %RANDOM
Rwork0.1872 ---
obs0.1898 13541 98.44 %-
all-14219 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.729 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.4092 Å20 Å20 Å2
2--11.297 Å2-0 Å2
3---2.1122 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 12 103 2520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082488
X-RAY DIFFRACTIONf_angle_d1.0863364
X-RAY DIFFRACTIONf_dihedral_angle_d14.934907
X-RAY DIFFRACTIONf_chiral_restr0.076354
X-RAY DIFFRACTIONf_plane_restr0.004434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47750.29191470.20832529X-RAY DIFFRACTION100
2.4775-2.72670.28011380.21282563X-RAY DIFFRACTION100
2.7267-3.12090.29491500.20812565X-RAY DIFFRACTION99
3.1209-3.93060.26691070.19552545X-RAY DIFFRACTION96
3.9306-29.85740.1871360.16352661X-RAY DIFFRACTION97

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