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Yorodumi- PDB-7xea: T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xea | ||||||
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Title | T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking | ||||||
Components | Endolysin | ||||||
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 | 7xea.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xea.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xea_validation.pdf.gz | 440.1 KB | Display | wwPDB validaton report |
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Full document | 7xea_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 7xea_validation.xml.gz | 12 KB | Display | |
Data in CIF | 7xea_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/7xea ftp://data.pdbj.org/pub/pdb/validation_reports/xe/7xea | HTTPS FTP |
-Related structure data
Related structure data | 7xe5C 7xe6C 7xe7C 7xe9C 5vnrS C: citing same article (ref.) S: Starting model for refinement |
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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 | ChemComp-NA / #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: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: A crystal was soaked into the precipitant-free solutions containing 40% DMSO, and then backsoaked into the precipitant-free solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2007 |
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→35.4 Å / Num. obs: 81025 / % possible obs: 98.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 11.94 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.062 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7157 / CC1/2: 0.812 / Rrim(I) all: 0.63 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VNR Resolution: 1.1→25.05 Å / SU ML: 0.0875 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7436 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: 18.84 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→25.05 Å
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Refine LS restraints |
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LS refinement shell |
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