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- PDB-2fgn: Structural Studies Examining the Substrate Specificity Profiles o... -

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Basic information

Entry
Database: PDB / ID: 2fgn
TitleStructural Studies Examining the Substrate Specificity Profiles of PC-PLCBc Protein Variants
ComponentsPhospholipase C
KeywordsHYDROLASE / PC-PLCBc protein variants / substrate specificity
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
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsBenfield, A.P. / Martin, S.F.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural studies examining the substrate specificity profiles of PC-PLC(Bc) protein variants.
Authors: Benfield, A.P. / Goodey, N.M. / Phillips, L.T. / Martin, S.F.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: 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 / 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)28,5584
Polymers28,3611
Non-polymers1963
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.522, 90.522, 70.214
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: 28361.348 Da / Num. of mol.: 1 / Mutation: Y56T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: plc / Plasmid: malE / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 45% saturated ammonium sulfate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19621 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.054 / Χ2: 1.114
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.070.1119050.98195.3
2.07-2.150.09519581.38498.1
2.15-2.250.08418480.95892.7
2.25-2.370.07218681.21694
2.37-2.520.07219891.14998.7
2.52-2.710.06819911.06299.2
2.71-2.990.0620141.08799.1
2.99-3.420.05419981.08898.5
3.42-4.30.04119411.17593
4.3-200.03821091.0396

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Phasing

Phasing MRRfactor: 0.388 / Cor.coef. Fo:Fc: 0.629
Highest resolutionLowest resolution
Rotation3 Å19.45 Å
Translation3 Å19.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 946 4.9 %5% of data
Rwork0.179 ---
all0.25 18461 --
obs0.22 18461 96.5 %-
Solvent computationBsol: 60.881 Å2
Displacement parametersBiso mean: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.871 Å20 Å20 Å2
2--0.871 Å20 Å2
3----1.742 Å2
Refinement stepCycle: LAST / Resolution: 2.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 3 171 2162
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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