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- PDB-1gym: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX WITH GLU... -

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Basic information

Entry
Database: PDB / ID: 1gym
TitlePHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX WITH GLUCOSAMINE-(ALPHA-1-6)-MYO-INOSITOL
ComponentsPHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
KeywordsHYDROLASE (PHOSPHORIC DIESTER) / PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C / GLUCOSAMINYL (ALPHA-1-6)-D-MYO-INOSITOL / INHIBITOR COMPLEX / LIPID DEGRADATION
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
Chem-MYG / 1-phosphatidylinositol phosphodiesterase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHeinz, D.W. / Ryan, M. / Smith, M.P. / Weaver, L.H. / Keana, J.F.W. / Griffith, O.H.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with glucosaminyl(alpha 1-->6)-D-myo-inositol, an essential fragment of GPI anchors.
Authors: Heinz, D.W. / Ryan, M. / Smith, M.P. / Weaver, L.H. / Keana, J.F. / Griffith, O.H.
#1: Journal: Embo J. / Year: 1995
Title: Crystal Structure of the Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus in Complex with Myo-Inositol
Authors: Heinz, D.W. / Ryan, M. / Bullock, T.L. / Griffith, O.H.
#2: Journal: Biophys.J. / Year: 1993
Title: Crystallization of Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus
Authors: Bullock, T.L. / Ryan, M. / Kim, S.L. / Remington, S.J. / Griffith, O.H.
#3: Journal: J.Bacteriol. / Year: 1989
Title: Phosphatidylinositol-Specific Phospholipase C of Bacillus Cereus: Cloning, Sequencing, and Relationship to Other Phospholipases
Authors: Kuppe, A. / Evans, L.M. / Mcmillen, D.A. / Griffith, O.H.
History
DepositionMay 2, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9102
Polymers34,5691
Non-polymers3411
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 46.500, 161.000
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 PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C


Mass: 34568.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: PI-PLC GENE / Plasmid: PBR322 RELATED / Gene (production host): PI-PLC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P14262, EC: 3.1.4.10
#2: Sugar ChemComp-MYG / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside / GLUCOSAMINYL-(ALPHA-6)-D-MYO-INOSITOL / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucoside / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-D-glucoside / (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-glucoside


Type: D-saccharide / Mass: 341.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H23NO10
IdentifierTypeProgram
glucosaminyl-(alpha-6)-D-myo-inositolIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlPI-PLC1drop
215 mMGlcN(alpha1-6)Ins.1drop
320 mMHEPES1drop
40.005 %1dropNaN3
518.5 %PEG6001drop
60.095 Mtrisodium citrate1drop
71.25 mMbeta-mercaptoethanol1drop
82.25 M1reservoirNaCl

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Jul 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 15359 / % possible obs: 72.4 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
% possible obs: 75 % / Num. measured all: 32130 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.22 Å / % possible obs: 62.2 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DETECTORSUPPLIED SOFTWAREdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→8 Å / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.272 -10 %
Rwork0.178 --
obs0.178 14670 75 %
Displacement parametersBiso mean: 20.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2991 0 0 137 3128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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