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Yorodumi- PDB-3a95: Crystal structure of hen egg white lysozyme soaked with 100mM RhC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a95 | ||||||
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Title | Crystal structure of hen egg white lysozyme soaked with 100mM RhCl3 at pH3.8 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Abe, S. / Koshiyama, T. / Ohki, T. / Hikage, T. / Watanabe, Y. / Ueno, T. | ||||||
Citation | Journal: Chemistry / Year: 2010 Title: Elucidation of Metal-Ion Accumulation Induced by Hydrogen Bonds on Protein Surfaces by Using Porous Lysozyme Crystals Containing Rh(III) Ions as the Model Surfaces Authors: Ueno, T. / Abe, S. / Koshiyama, T. / Ohki, T. / Hikage, T. / Watanabe, Y. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a95.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a95.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 3a95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a95_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 3a95_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 3a95_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3a95_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/3a95 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/3a95 | HTTPS FTP |
-Related structure data
Related structure data | 3a8zC 3a90C 3a91C 3a92C 3a93C 3a94C 3a96C 193lS 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: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | #4: Chemical | ChemComp-RH3 / #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: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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 VII / Detector: IMAGE PLATE / Date: Feb 5, 2009 |
Radiation | Monochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→80 Å / Num. obs: 18981 / % possible obs: 99.9 % / Redundancy: 24.4 % / Biso Wilson estimate: 18.672 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.319 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.5→20.57 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.357 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.627 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.499→1.538 Å / Total num. of bins used: 20
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