+Open data
-Basic information
Entry | Database: PDB / ID: 1w6z | ||||||
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Title | High Energy Tetragonal Lysozyme X-ray Structure | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / LYSOZYME / HIGH / ENERGY / HOLMIUM / KEDGE / BACTERIOLYTIC ENZYME / GLYCOSIDASE | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | GALLUS GALLUS (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Jakoncic, J. / Aslantas, M. / Honkimaki, V. / Di Michiel, M. / Stojanoff, V. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2006 Title: Anomalous Diffraction at Ultra-High Energy for Protein Crystallography. Authors: Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w6z.cif.gz | 44.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w6z.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1w6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/1w6z ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w6z | HTTPS FTP |
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-Related structure data
Related structure data | 2bpuC 2cgiC 194lS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: HYDROLYSIS OF THE 1,4-BETA-LINKAGES BETWEEN N- ACETYL-D-GLUCOSAMINE AND N- ...CATALYTIC ACTIVITY: HYDROLYSIS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.78 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.5 Details: HANGING DROP METHOD, 0.3M HOCL3, 0.9M NACL, 0.05M SODIUM ACETATE PH4.5, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID15A / Wavelength: 0.2228 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.2228 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25 Å / Num. obs: 25272 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 194L Resolution: 1.65→24.49 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 579327.81 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5887 Å2 / ksol: 0.362113 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→24.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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