+Open data
-Basic information
Entry | Database: PDB / ID: 1p6y | ||||||
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Title | T4 LYSOZYME CORE REPACKING MUTANT M120Y/TA | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / DESIGNED CORE MUTANT / AUTOMATED PROTEIN DESIGN / PROTEIN ENGINEERING / PROTEIN FOLDING / PROTEIN STABILITY / CORE REPACKING / BACK REVERTANT / DEAD-END ELIMINATION THEOREM / SIDE-CHAIN PACKING / OPTIMIZED ROTAMER COMBINATIONS / ORBIT | ||||||
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: 1.54 Å | ||||||
Authors | Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Repacking the Core of T4 Lysozyme by Automated Design Authors: Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.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 | 1p6y.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p6y.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 1p6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p6y ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p6y | HTTPS FTP |
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-Related structure data
Related structure data | 1p2lC 1p2rC 1p36C 1p37C 1p3nC 1p46C 1p64C 1p7sC 1pqdC 1pqiC 1pqjC 1pqkC 1pqmC 1pqoC 1l63S C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18660.342 Da / Num. of mol.: 1 / Mutation: C54T, C97A, M120Y 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 / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme |
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-Non-polymers , 5 types, 197 molecules
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-K / | ||||
#4: Chemical | #5: Chemical | ChemComp-HED / | #6: 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: 2.71 Å3/Da / Density % sol: 54.32 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: K/Na Phosphate, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
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
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 31, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→22.894 Å / Num. all: 29398 / Num. obs: 29398 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 20.556 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3205 / Rsym value: 0.252 / % possible all: 97.7 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L63 Resolution: 1.54→22 Å / Isotropic thermal model: TNT / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT Details: The working set and the test set were not combined in the last cycles of refinement. The overall anisotropic B values are as follows: B11=B12=B22= 1.85, B13=B23=0.0, B33 = -3.69
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Solvent computation | Solvent model: TNT / Bsol: 148.044 Å2 / ksol: 0.7167 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.54→22 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.4 |