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Yorodumi- PDB-1t6h: Crystal Structure T4 Lysozyme incorporating an unnatural amino ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6h | ||||||
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Title | Crystal Structure T4 Lysozyme incorporating an unnatural amino acid p-iodo-L-phenylalanine at position 153 | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / IodoPhe / SAD Phasing / UNNATURAL AMINO ACID | ||||||
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 / SAD / Resolution: 2.01 Å | ||||||
Authors | Spraggon, G. / Xie, J. / Wang, L. / Wu, N. / Brock, A. / Schultz, P.G. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2004 Title: The site-specific incorporation of p-iodo-L-phenylalanine into proteins for structure determination. Authors: Xie, J. / Wang, L. / Wu, N. / Brock, A. / Spraggon, G. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6h.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6h.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6h ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6h | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 18788.363 Da / Num. of mol.: 1 / Mutation: F153(PIL) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: pT4153TAG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00720, lysozyme | ||||
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#2: Chemical | #3: Chemical | #4: 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: 2.67 Å3/Da / Density % sol: 55 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 Details: 0.25M NaCl. 2.0M Na/K phosphate buffer, 15mM hydroxyethyl disulfide, pH 6.7, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 4, 2003 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→100 Å / Num. all: 13753 / Num. obs: 13753 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 110.33 |
Reflection shell | Resolution: 2.01→2.1 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 64 / Num. unique all: 1345 / Rsym value: 0.128 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.01→84.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.894 / SU ML: 0.082 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.933 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→84.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.064 Å / Total num. of bins used: 20 /
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