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- PDB-4i9j: Structure of the N254Y/H258Y mutant of the phosphatidylinositol-s... -

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Basic information

Entry
Database: PDB / ID: 4i9j
TitleStructure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus bound to diC4PC
Components1-phosphatidylinositol phosphodiesterase
Keywordshydrolase / lyase / TIM barrel / phospholipase / diC4PC binding
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 / Chem-XP5 / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGoldstein, R.I. / Cheng, J. / Stec, B. / Gershenson, A. / Roberts, M.F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The cation-pi box is a specific phosphatidylcholine membrane targeting motif.
Authors: Cheng, J. / Goldstein, R. / Gershenson, A. / Stec, B. / Roberts, M.F.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 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)36,8235
Polymers35,3161
Non-polymers1,5074
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.649, 57.473, 61.752
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 / 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-XP5 / (4S,7R)-7-(heptanoyloxy)-4-hydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphahexadecan-1-aminium 4-oxide


Mass: 482.568 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H45NO8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 27% PEG 4000, 0.1M sodium acetate, 0.1M magnesium nitrate, 0.15M ammonium acetate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 26, 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: 1.85→50 Å / Num. all: 230045 / Num. obs: 230045 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 47.395
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.823 / Num. unique all: 749 / Rsym value: 0.789 / % possible all: 57.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V18

3v18


Resolution: 1.85→37.761 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1279 5.17 %RANDOM
Rwork0.1602 ---
obs0.1627 24758 92.49 %-
all-24758 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→37.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 82 230 2729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192610
X-RAY DIFFRACTIONf_angle_d1.9433537
X-RAY DIFFRACTIONf_dihedral_angle_d17.8661024
X-RAY DIFFRACTIONf_chiral_restr0.131361
X-RAY DIFFRACTIONf_plane_restr0.01442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8482-1.92220.3652940.26461701X-RAY DIFFRACTION61
1.9222-2.00970.25951140.1992283X-RAY DIFFRACTION82
2.0097-2.11560.25211400.15552702X-RAY DIFFRACTION97
2.1156-2.24810.27221440.22710X-RAY DIFFRACTION97
2.2481-2.42170.23771700.1692690X-RAY DIFFRACTION98
2.4217-2.66540.23441350.15262789X-RAY DIFFRACTION99
2.6654-3.05090.22151720.15782777X-RAY DIFFRACTION99
3.0509-3.84320.18531610.15342838X-RAY DIFFRACTION99
3.8432-37.76930.16461490.14762989X-RAY DIFFRACTION100

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