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Yorodumi- PDB-5kki: 1.7-Angstrom in situ Mylar structure of hen egg-white lysozyme (H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kki | |||||||||
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Title | 1.7-Angstrom in situ Mylar structure of hen egg-white lysozyme (HEWL) at 100 K | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE | |||||||||
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: 1.7 Å | |||||||||
Authors | Broecker, J. / Ernst, O.P. | |||||||||
Funding support | Canada, Germany, 2items
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Citation | Journal: Cryst Growth Des / Year: 2016 Title: A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Authors: Broecker, J. / Klingel, V. / Ou, W.L. / Balo, A.R. / Kissick, D.J. / Ogata, C.M. / Kuo, A. / Ernst, O.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kki.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kki.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 5kki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/5kki ftp://data.pdbj.org/pub/pdb/validation_reports/kk/5kki | HTTPS FTP |
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-Related structure data
Related structure data | 5kkhC 5kkjC 5kkkC 4zixS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 128 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-PE5 / | #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: 2.05 Å3/Da / Density % sol: 39.9 % / Description: cubes and rods |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.5 / Details: 100 mM NaOAc, 1 M NaCl, 30% (v/v) PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.91 Å / Num. obs: 12515 / % possible obs: 92 % / Redundancy: 1.9 % / Biso Wilson estimate: 19.33 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Net I/σ(I): 4.28 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 1.38 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZIX Resolution: 1.7→38.91 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 18.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.91 Å
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Refine LS restraints |
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LS refinement shell |
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