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- PDB-3v16: An intramolecular pi-cation latch in phosphatidylinositol-specifi... -

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Basic information

Entry
Database: PDB / ID: 3v16
TitleAn intramolecular pi-cation latch in phosphatidylinositol-specific phospholipase C from S.aureus controls substrate access to the active site
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / pi-cation / TIM barrel / 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
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: 2.05 Å
AuthorsGoldstein, R.I. / Cheng, J. / Stec, B. / Roberts, M.F.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of the S. aureus PI-Specific Phospholipase C Reveals Modulation of Active Site Access by a Titratable PI-Cation Latched Loop
Authors: Goldstein, R. / Cheng, J. / Stec, B. / Roberts, M.F.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 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)34,5003
Polymers34,2841
Non-polymers2162
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.161, 43.607, 62.218
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: 34284.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG 4000, 0.15 M ammonium acetate, 0.1 M sodium acetate, 0.01M 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: Mar 4, 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
ReflectionResolution: 2.05→50 Å / Num. all: 18544 / Num. obs: 18080 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6 % / % possible all: 77.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PTG

1ptg


Resolution: 2.05→39.94 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.368 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21314 923 5.1 %RANDOM
Rwork0.15552 ---
obs0.15844 17112 97.4 %-
all-13127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 13 225 2656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222519
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9463416
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17525.366123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18115436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.492156
X-RAY DIFFRACTIONr_chiral_restr0.1230.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021927
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1241.51517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.96222447
X-RAY DIFFRACTIONr_scbond_it3.2531002
X-RAY DIFFRACTIONr_scangle_it4.9814.5964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 49 -
Rwork0.192 1016 -
obs--79.54 %

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