+Open data
-Basic information
Entry | Database: PDB / ID: 5jgn | ||||||
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Title | Spin-Labeled T4 Lysozyme Construct I9V1 | ||||||
Components | Endolysin | ||||||
Keywords | HYDROLASE / Spin label / EPR / DEER | ||||||
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 sensu lato (virus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.534 Å | ||||||
Authors | Balo, A.R. / Feyrer, H. / Ernst, O.P. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Biochemistry / Year: 2016 Title: Toward Precise Interpretation of DEER-Based Distance Distributions: Insights from Structural Characterization of V1 Spin-Labeled Side Chains. Authors: Balo, A.R. / Feyrer, H. / Ernst, O.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jgn.cif.gz | 57.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jgn.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jgn_validation.pdf.gz | 772.3 KB | Display | wwPDB validaton report |
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Full document | 5jgn_full_validation.pdf.gz | 772.8 KB | Display | |
Data in XML | 5jgn_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 5jgn_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/5jgn ftp://data.pdbj.org/pub/pdb/validation_reports/jg/5jgn | HTTPS FTP |
-Related structure data
Related structure data | 5jgrC 5jguC 5jgvC 5jgxC 5jgzC 5kgrC 1c6tS C: citing same article (ref.) 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: 18618.348 Da / Num. of mol.: 1 / Mutation: I9C, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 sensu lato (virus) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00720, lysozyme |
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-Non-polymers , 5 types, 339 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-V1A / | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop Details: sodium/potassium phosphate, sodium chloride, hexane-1,6-diol, 2-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Sep 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.534→29.91 Å / Num. obs: 30273 / % possible obs: 100 % / Redundancy: 2 % / Net I/σ(I): 20.09 |
Reflection shell | Highest resolution: 1.534 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1C6T Resolution: 1.534→29.91 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.534→29.91 Å
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Refine LS restraints |
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LS refinement shell |
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