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- PDB-1p6e: STRUCTURE OF THE D55N MUTANT OF PHOSPHOLIPASE C FROM BACILLUS CER... -

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Basic information

Entry
Database: PDB / ID: 1p6e
TitleSTRUCTURE OF THE D55N MUTANT OF PHOSPHOLIPASE C FROM BACILLUS CEREUS IN COMPLEX WITH 1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE
ComponentsPhospholipase C
KeywordsHYDROLASE / PROTEIN-PHOSPHOLIPID ANALOGUE COMPLEX / TRI ZN+2 METAL CORE
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / killing of cells of another organism / zinc ion binding
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PC5 / Phospholipase C
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsAntikainen, N.M. / Monzingo, A.F. / Franklin, C.L. / Robertus, J.D. / Martin, S.F.
CitationJournal: Arch.Biochem.Biophys. / Year: 2003
Title: Using X-ray crystallography of the Asp55Asn mutant of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus to support the mechanistic role of Asp55 as the general base.
Authors: Antikainen, N.M. / Monzingo, A.F. / Franklin, C.L. / Robertus, J.D. / Martin, S.F.
History
DepositionApr 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0765
Polymers28,4221
Non-polymers6544
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.795, 89.795, 74.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phospholipase C / PLC / Phosphatidylcholine cholinephosphohydrolase / Cereolysin A


Mass: 28422.436 Da / Num. of mol.: 1 / Mutation: D55N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: PLC / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P09598, phospholipase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PC5 / 1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE


Mass: 457.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36NO6PS2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: AMMOUNIUM SULPHATE, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.75 mg/mlprotein1drop
224.6 %satammonium sulfate1drop
340 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 24, 2000 / Details: MIRRORS
RadiationMonochromator: DOUBLE FOCUSING MIRRORS (NI&PT) + NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13590 / Num. obs: 13590 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.302 / % possible all: 99.7
Reflection
*PLUS
Reflection shell
*PLUS
Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ID 1AH7

1ah7


Resolution: 2.3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1269 -RANDOM
Rwork0.163 ---
all0.167 12581 --
obs0.167 12581 98.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 31 72 2116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.321
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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