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- PDB-4f2b: Modulation of S.Aureus Phosphatidylinositol-Specific Phospholipas... -

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Basic information

Entry
Database: PDB / ID: 4f2b
TitleModulation of S.Aureus Phosphatidylinositol-Specific Phospholipase C Membrane Binding
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / Dimer / Phosphatidylinositol-specific Phospholipase C
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 speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 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 7, 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
B: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8454
Polymers70,4842
Non-polymers3602
Water2,216123
1
A: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4222
Polymers35,2421
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1-phosphatidylinositol phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4222
Polymers35,2421
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.362, 133.382, 50.190
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35242.141 Da / Num. of mol.: 2 / Fragment: UNP residues 11-312
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-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG 4000, 0.150 M ammonium acetate, 0.100 M sodium acetate, 0.001 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: Dec 19, 2011 / Details: Osmic VariMax
RadiationMonochromator: RIGAKU MICROMAX-07 HF MICROFOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.545
11-h,-k,l20.455
ReflectionResolution: 2.16→50 Å / Num. all: 116278 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 3.9 % / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3V16

3v16


Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.296 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R: 0.043 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25047 1534 5.3 %RANDOM
Rwork0.21471 ---
obs0.21673 27485 95.37 %-
all-29019 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.531 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å20 Å2-1.54 Å2
2---4.12 Å20 Å2
3---9.23 Å2
Refinement stepCycle: LAST / Resolution: 2.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 24 123 4988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg2.1
X-RAY DIFFRACTIONr_bond_refined_d0.008
LS refinement shellResolution: 2.16→2.218 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 84 -
Rwork0.278 1674 -
obs--79.26 %

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