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- PDB-2or2: Structure of the W47A/W242A Mutant of Bacterial Phosphatidylinosi... -

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Basic information

Entry
Database: PDB / ID: 2or2
TitleStructure of the W47A/W242A Mutant of Bacterial Phosphatidylinositol-Specific Phospholipase C
Components1-phosphatidylinositol phosphodiesterase
KeywordsLYASE / phosphatidylinositol-specific phospholipase C / PI-PLC / Dimer / interfacially impaired / membrane binding / TIM barrel
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 speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsShao, C. / Shi, X. / Wehbi, H. / Zambonelli, C. / Head, J.F. / Seaton, B.A. / Roberts, M.F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Dimer structure of an interfacially impaired phosphatidylinositol-specific phospholipase C.
Authors: Shao, C. / Shi, X. / Wehbi, H. / Zambonelli, C. / Head, J.F. / Seaton, B.A. / Roberts, M.F.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)68,1222
Polymers68,1222
Non-polymers00
Water10,377576
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.424, 70.028, 154.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are two monomers in the asymmetric unit. The two monomers follow a pseudo 2-fold symmetry

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Components

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


Mass: 34060.996 Da / Num. of mol.: 2 / Mutation: W47A, W242A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P08954, phosphatidylinositol diacylglycerol-lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 5.4
Details: 15% 2-methyl-2,4-pentanediol, 16% PEG400, pH 5.4, vapor diffusion, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorDetector: CCD / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 60615 / % possible obs: 98.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.042 / Χ2: 1.152 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.84-1.882.30.15836461.43990.6
1.88-1.932.90.15138981.45996.7
1.93-1.983.30.1338951.42996.9
1.98-2.044.50.12340321.43199.7
2.04-2.114.70.10240201.43699.7
2.11-2.184.80.08840281.38499.6
2.18-2.274.90.07740661.31199.7
2.27-2.374.70.06640191.25399.6
2.37-2.54.80.05840881.18599.9
2.5-2.654.80.04940611.113100
2.65-2.864.80.04240781.039100
2.86-3.154.80.03641090.95100
3.15-3.64.80.03141410.824100
3.6-4.544.70.02941850.73499.9
4.54-504.40.0343490.80899.3

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Phasing

Phasing MRRfactor: 0.52 / Cor.coef. Fo:Fc: 0.356
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.215 4788 7.8 %
Rwork0.186 --
obs-58605 95.6 %
Solvent computationBsol: 42.412 Å2
Displacement parametersBiso mean: 23.23 Å2
Baniso -1Baniso -2Baniso -3
1--8.306 Å20 Å20 Å2
2--0.732 Å20 Å2
3---7.573 Å2
Refinement stepCycle: LAST / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 0 576 5382
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3231.5
X-RAY DIFFRACTIONc_scbond_it1.9372
X-RAY DIFFRACTIONc_mcangle_it2.0932
X-RAY DIFFRACTIONc_scangle_it2.8842.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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