+Open data
-Basic information
Entry | Database: PDB / ID: 6ph0 | ||||||
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Title | T4 lysozyme pseudo-wild type soaked in TEMPO | ||||||
Components | Endolysin | ||||||
Keywords | HYDROLASE / T4 Lysozyme / MTSL / spin label | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.947 Å | ||||||
Authors | Cuneo, M.J. / Myles, D.A. / Li, L. | ||||||
Citation | Journal: To be published Title: Making hydrogens stand out: Enhanced neutron diffraction from biological crystals using dynamic nuclear polarization Authors: Pierce, J. / Myles, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ph0.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ph0.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ph0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ph0_validation.pdf.gz | 349.8 KB | Display | wwPDB validaton report |
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Full document | 6ph0_full_validation.pdf.gz | 387.5 KB | Display | |
Data in XML | 6ph0_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 6ph0_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/6ph0 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/6ph0 | HTTPS FTP |
-Related structure data
Related structure data | 6pgyC 6pgzC 6ph1C 5vnrS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 18628.363 Da / Num. of mol.: 1 / Mutation: C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: D9IEF7, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HED / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 2.0M Na/K Phosphate, 250mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.947→20 Å / Num. obs: 14827 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.151 / Χ2: 1.144 / Net I/av σ(I): 11.5 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VNR Resolution: 1.947→19.527 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.91 Å2 / Biso mean: 21.8984 Å2 / Biso min: 11.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.947→19.527 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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