+Open data
-Basic information
Entry | Database: PDB / ID: 1lpy | ||||||
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Title | Multiple Methionine Substitutions in T4 Lysozyme | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / hydrolase (o-glycosyl) / T4 lysozyme / methionine core mutant / protein engineering / protein folding | ||||||
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: 1.65 Å | ||||||
Authors | Gassner, N.C. / Baase, W.A. / Mooers, B.H.M. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / Matthews, B.W. | ||||||
Citation | Journal: Biophys.Chem. / Year: 2003 Title: Multiple methionine substitutions are tolerated in T4 lysozyme and have coupled effects on folding and stability. Authors: Gassner, N.C. / Baase, W.A. / Mooers, B.H. / Busam, R.D. / Weaver, L.H. / Lindstrom, J.D. / Quillin, M.L. / 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 | 1lpy.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpy.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lpy_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 1lpy_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 1lpy_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1lpy_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpy ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpy | HTTPS FTP |
-Related structure data
Related structure data | 1ks3C 1kw5C 1kw7C 1ky0C 1ky1C 1l0jC 1l0kC 1lw9C 1lwgC 1lwkC 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: 19654.395 Da / Num. of mol.: 1 Mutation: C54T,L84M,V87M,L91M,C97A,L99M,I100M,V103M,G110R,V111M,L118M,L121M,L133M 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: phs1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-BME / |
#5: 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: 2.48 Å3/Da / Density % sol: 50.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion / Details: Eriksson, A.E., (1993) J. Mol. Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.65→15 Å / Num. all: 23682 / Num. obs: 23682 / % possible obs: 95 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.65→1.74 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1878 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Native T4 Lysozyme Resolution: 1.65→15 Å / σ(F): 0 / Stereochemistry target values: TNT Details: Residues ASN 163 and LEU 164 are missing in the electron density.
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Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / Rfactor all: 0.209 / Rfactor obs: 0.207 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: t_bond_d / Dev ideal: 0.017 |