+Open data
-Basic information
Entry | Database: PDB / ID: 1pqd | ||||||
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Title | T4 LYSOZYME CORE REPACKING MUTANT CORE10/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: 1.65 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 | 1pqd.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pqd.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 1pqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pqd_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 1pqd_full_validation.pdf.gz | 434.7 KB | Display | |
Data in XML | 1pqd_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1pqd_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqd ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqd | HTTPS FTP |
-Related structure data
Related structure data | 1p2lC 1p2rC 1p36C 1p37C 1p3nC 1p46C 1p64C 1p6yC 1p7sC 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
#1: Protein | Mass: 18656.309 Da / Num. of mol.: 1 Mutation: C54T/V87I/C97A/I100V/M102L/V103I/M106I/V111A/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: 2.69 Å3/Da / Density % sol: 54.26 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 Details: Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 100K | ||||||||||||||||||||||||||||||
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 RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000 / 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: 1.65→16.3 Å / Num. all: 23982 / Num. obs: 23982 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 85 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L63 Resolution: 1.65→16.3 Å Cross valid method: Fo-Fo maps with wild-type structure factors and phases σ(F): 0 / Stereochemistry target values: TNT stereochemistry values / Details: Free R was not used in the refinement /
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Solvent computation | Solvent model: TNT / Bsol: 139.274 Å2 / ksol: 0.9486 e/Å3 | ||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→16.3 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rwork: 0.178 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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