+Open data
-Basic information
Entry | Database: PDB / ID: 8cqm | |||||||||
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Title | Broad-range phospholipase C from Listeria monocytogenes | |||||||||
Components | Phospholipase C | |||||||||
Keywords | HYDROLASE / Zinc-binding / monomer / phospholipase / listeria / lipids / membrane / virulence factor | |||||||||
Function / homology | Function and homology information phospholipase C / phosphatidylcholine phospholipase C activity / zinc ion binding Similarity search - Function | |||||||||
Biological species | Listeria monocytogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | |||||||||
Authors | Petrisic, N. / Podobnik, M. | |||||||||
Funding support | Slovenia, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for the unique molecular properties of broad-range phospholipase C from Listeria monocytogenes. Authors: Petrisic, N. / Adamek, M. / Kezar, A. / Hocevar, S.B. / Zagar, E. / Anderluh, G. / Podobnik, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cqm.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cqm.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cqm_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 8cqm_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 8cqm_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 8cqm_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqm ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqm | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Experimental dataset #1 | Data reference: 10.51093/xrd-00127 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper:
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-Components
#1: Protein | Mass: 27716.740 Da / Num. of mol.: 2 / Mutation: C143S, C168S Source method: isolated from a genetically manipulated source Details: gene obtained from genomic isolate of L. monocytogenes Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: plcB, prtC, lmo0205 / Plasmid: pTYB21 / Details (production host): from NEB Impact system / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33378, phospholipase C #2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-FE / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8K Na-citrate isopropanol, trimethylamine-N-oxide, phoscholine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.26 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.26 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.94 Å / Num. obs: 53274 / % possible obs: 99.6 % / Redundancy: 14.5 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 1 / Rrim(I) all: 0.089 / Net I/σ(I): 27.07 |
Reflection shell | Resolution: 2→2.12 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 4.26 / Num. unique obs: 8615 / CC1/2: 0.934 / Rrim(I) all: 0.0657 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→41.46 Å / SU ML: 0.2009 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.2414 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.46 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.00221779466 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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