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- PDB-4f2u: Structure of the N254Y/H258Y double mutant of the Phosphatidylino... -

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Basic information

Entry
Database: PDB / ID: 4f2u
TitleStructure of the N254Y/H258Y double mutant of the Phosphatidylinositol-Specific Phospholipase C from S.aureus
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / alpha beta barrel / Phosphatidylinositol-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 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
1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 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)35,8894
Polymers35,3161
Non-polymers5733
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.220, 56.119, 61.708
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: 35316.238 Da / Num. of mol.: 1 / Fragment: UNP residues 11-312 / Mutation: N254Y/H258Y
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 4000,0.100 M Hepes, 10% isopropanol, pH 7.5, 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: Aug 15, 2011 / 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: 2.19→50 Å / Num. all: 94114 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 26.49
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 6 % / % possible all: 100

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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: 2.19→30.854 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 795 5 %Random
Rwork0.158 ---
obs0.1618 15898 99.52 %-
all-16693 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.447 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5575 Å2-0 Å20 Å2
2---1.3503 Å2-0 Å2
3---3.9077 Å2
Refinement stepCycle: LAST / Resolution: 2.19→30.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 35 288 2759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192530
X-RAY DIFFRACTIONf_angle_d1.7033421
X-RAY DIFFRACTIONf_dihedral_angle_d15.729931
X-RAY DIFFRACTIONf_chiral_restr0.109354
X-RAY DIFFRACTIONf_plane_restr0.007432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.32750.25381350.16952424X-RAY DIFFRACTION98
2.3275-2.50710.27291400.17092472X-RAY DIFFRACTION100
2.5071-2.75930.26921300.16552491X-RAY DIFFRACTION100
2.7593-3.15820.25241380.17122505X-RAY DIFFRACTION100
3.1582-3.97770.21111330.15732539X-RAY DIFFRACTION100
3.9777-30.8570.22111190.14542672X-RAY DIFFRACTION100

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