+Open data
-Basic information
Entry | Database: PDB / ID: 1pqi | ||||||
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Title | T4 LYSOZYME CORE REPACKING MUTANT I118L/CORE7/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: 1.57 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 | 1pqi.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pqi.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pqi_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 1pqi_full_validation.pdf.gz | 448.4 KB | Display | |
Data in XML | 1pqi_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1pqi_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqi ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqi | HTTPS FTP |
-Related structure data
Related structure data | 1p2lC 1p2rC 1p36C 1p37C 1p3nC 1p46C 1p64C 1p6yC 1p7sC 1pqdC 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
#1: Protein | Mass: 18724.449 Da / Num. of mol.: 1 / Mutation: C54T/I78V/V87M/C97A/L118I/M120Y/L133F/V149I/T152V 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-K / | ||||
#3: Chemical | #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: 2.67 Å3/Da / Density % sol: 53.59 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 6.7 Details: 2 M Na/K Phosphate, 550 mM NaCl, 40 mM BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70 | ||||||||||||||||||||||||||||||
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: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 11, 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: 1.57→22.82 Å / Num. obs: 29013 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 20.67 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.57→1.64 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.204 / % possible all: 90.7 |
Reflection | *PLUS % possible obs: 91.1 % |
Reflection shell | *PLUS % possible obs: 91 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L63 Resolution: 1.57→22.83 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT / Details: WORKING AND TEST SET NOT COMBINED
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Solvent computation | Solvent model: TNT / Bsol: 215.387 Å2 / ksol: 0.85 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→22.83 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.56 Å / Rfactor Rwork: 0.198 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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