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Yorodumi- PDB-5lwo: Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lwo | ||||||
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Title | Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K | ||||||
Components | Endolysin | ||||||
Keywords | HYDROLASE / NITROXIDE / SPIN LABEL / T4 LYSOZYME / ELECTRON PARAMAGNETIC RESONANCE / EPR | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.183 Å | ||||||
Authors | Loll, B. / Consentius, P. / Gohlke, U. / Mueller, R. / Kaupp, M. / Heinemann, U. / Wahl, M.C. / Risse, T. | ||||||
Citation | Journal: J Phys Chem Lett / Year: 2017 Title: Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins. Authors: Consentius, P. / Loll, B. / Gohlke, U. / Alings, C. / Muller, C. / Muller, R. / Teutloff, C. / Heinemann, U. / Kaupp, M. / Wahl, M.C. / Risse, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lwo.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lwo.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 5lwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lwo_validation.pdf.gz | 467.6 KB | Display | wwPDB validaton report |
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Full document | 5lwo_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | 5lwo_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 5lwo_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/5lwo ftp://data.pdbj.org/pub/pdb/validation_reports/lw/5lwo | HTTPS FTP |
-Related structure data
Related structure data | 5jdtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18576.350 Da / Num. of mol.: 1 / Mutation: C54T C97A L118C T115C R119C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pET28b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P00720, lysozyme |
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-Non-polymers , 7 types, 284 molecules
#2: Chemical | ChemComp-RXR / [ | ||||||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-HED / | #5: Chemical | ChemComp-PO4 / | #6: Chemical | ChemComp-BME / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 2.0 M NA/K PHOSPHATE, 240 mM NACL, 40 mM 2-HYDROXYETHYL DISULFIDE, PH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8946 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2015 / Details: Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8946 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 66752 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 11.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.18→1.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.772 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JDT Resolution: 1.183→18.299 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.183→18.299 Å
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Refine LS restraints |
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LS refinement shell |
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