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Yorodumi- PDB-3guj: T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3guj | ||||||
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Title | T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--Benzene binding | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / T4 lysozyme / apolar cavity / buried charge / ligand binding / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
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: 1.6 Å | ||||||
Authors | Liu, L. / Matthews, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Use of stabilizing mutations to engineer a charged group within a ligand-binding hydrophobic cavity in T4 lysozyme. Authors: Liu, L. / Baase, W.A. / Michael, M.M. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3guj.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3guj.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 3guj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3guj ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guj | HTTPS FTP |
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-Related structure data
Related structure data | 3guiSC 3gukC 3gulC 3gumC 3gunC 3guoC 3gupC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18709.568 Da / Num. of mol.: 1 / Mutation: T21C/S38D/L99A/M102E/E108V/S117V/T142C/N144D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: p1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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-Non-polymers , 6 types, 183 molecules
#2: Chemical | ChemComp-BNZ / |
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#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-CO3 / |
#5: Chemical | ChemComp-EPE / |
#6: Chemical | ChemComp-SO4 / |
#7: 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: 2.04 Å3/Da / Density % sol: 39.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 30% PEG 8000, 0.2M ammounium sulfate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2007 / Details: Si(111) |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.644 Å / Num. obs: 19653 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.9 / % possible all: 96.2 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GUI Resolution: 1.6→45.64 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.023 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.532 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.645 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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