+Open data
-Basic information
Entry | Database: PDB / ID: 7xe6 | ||||||
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Title | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7 | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / Intermolecular disulfide symmetry cross-linked crystal | ||||||
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 | Escherichia virus T4 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Tamada, T. / Hiromoto, T. | ||||||
Funding support | 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Creation of Cross-Linked Crystals With Intermolecular Disulfide Bonds Connecting Symmetry-Related Molecules Allows Retention of Tertiary Structure in Different Solvent Conditions. Authors: Hiromoto, T. / Ikura, T. / Honjo, E. / Blaber, M. / Kuroki, R. / Tamada, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xe6.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xe6.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xe6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/7xe6 ftp://data.pdbj.org/pub/pdb/validation_reports/xe/7xe6 | HTTPS FTP |
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-Related structure data
Related structure data | 7xe5C 7xe7C 7xe9C 7xeaC 5vnrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18667.572 Da / Num. of mol.: 1 / Mutation: S44C, C54T, N68C, A93C, C97A, T115C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia virus T4 / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, lysozyme | ||||||||
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#2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.7 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: A crystal was soaked into precipitant-free solutions (pH7). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→45.9 Å / Num. obs: 82294 / % possible obs: 99.5 % / Redundancy: 9.6 % / Biso Wilson estimate: 9.97 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.1→1.14 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8082 / CC1/2: 0.891 / Rrim(I) all: 0.609 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VNR Resolution: 1.1→25.52 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.6835 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→25.52 Å
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Refine LS restraints |
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LS refinement shell |
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