+Open data
-Basic information
Entry | Database: PDB / ID: 4w55 | ||||||
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Title | T4 Lysozyme L99A with n-Propylbenzene Bound | ||||||
Components | Endolysin | ||||||
Keywords | HYDROLASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6401 Å | ||||||
Authors | Merski, M. / Shoichet, B.K. / Eidam, O. / Fischer, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Homologous ligands accommodated by discrete conformations of a buried cavity. Authors: Merski, M. / Fischer, M. / Balius, T.E. / Eidam, O. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4w55.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4w55.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 4w55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4w55_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 4w55_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 4w55_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 4w55_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/4w55 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/4w55 | HTTPS FTP |
-Related structure data
Related structure data | 4w51C 4w52C 4w53C 4w54C 4w56C 4w57C 4w58C 4w59C 181lS S: Starting model for refinement 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: 19691.541 Da / Num. of mol.: 1 / Mutation: L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme |
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#2: Chemical | ChemComp-3H0 / |
#3: Chemical | ChemComp-EPE / |
#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: 2.57 Å3/Da / Density % sol: 52.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% (w/v) PEGF-4000, 10% 2-propanol, 0.1 M HEPES, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: two flat Si(111) crystals, mounted in a model DCM from Khozu Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.64→50 Å / Num. obs: 27463 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 15.83 Å2 / Rmerge F obs: 0.076 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.973 / Net I/σ(I): 23.64 / Num. measured all: 226432 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 181L Resolution: 1.6401→45.938 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.442 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63 Å2 / Biso mean: 17.5808 Å2 / Biso min: 7.82 Å2
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Refinement step | Cycle: final / Resolution: 1.6401→45.938 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %
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