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Yorodumi- PDB-3w6a: Crystal structure of cross-linked tetragonal hen egg white lysozy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w6a | ||||||
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Title | Crystal structure of cross-linked tetragonal hen egg white lysozyme soaked wiht 5mM [Ru(benzene)Cl2]2 | ||||||
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: 1.77 Å | ||||||
Authors | Tabe, H. / Abe, S. / Hikage, T. / Kitagawa, S. / Ueno, T. | ||||||
Citation | Journal: To be Published Title: Solid Artificial Metalloenzymes: Post-Engineering of Porous Protein Crystals by Organometallic Complexes Authors: Ueno, T. / Tabe, H. / Abe, S. / Hikage, T. / Kitagawa, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w6a.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w6a.ent.gz | 27.8 KB | Display | PDB format |
PDBx/mmJSON format | 3w6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/3w6a ftp://data.pdbj.org/pub/pdb/validation_reports/w6/3w6a | HTTPS FTP |
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-Related 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 6 types, 83 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-RBN / | #6: Chemical | ChemComp-RU / | #7: Water | ChemComp-HOH / | |
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-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: 37.92 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 25, 2010 |
Radiation | Monochromator: Fixed exit Si 111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30 Å / Num. obs: 29518 / % possible obs: 99 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1.77→1.82 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→27.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.11 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 30.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→27.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Total num. of bins used: 20
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