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Yorodumi- PDB-5hnl: In-house X-ray single crystal diffraction from protein microcryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hnl | ||||||
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Title | In-house X-ray single crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels | ||||||
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 / Resolution: 2.424 Å | ||||||
Authors | Tsukui, S. / Kimura, F. / Kusaka, K. / Baba, S. / Mizuno, N. / Kimura, T. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Neutron and X-ray single-crystal diffraction from protein microcrystals via magnetically oriented microcrystal arrays in gels. Authors: Tsukui, S. / Kimura, F. / Kusaka, K. / Baba, S. / Mizuno, N. / Kimura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hnl.cif.gz | 34 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hnl.ent.gz | 24.7 KB | Display | PDB format |
PDBx/mmJSON format | 5hnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/5hnl ftp://data.pdbj.org/pub/pdb/validation_reports/hn/5hnl | 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
#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: 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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 313 K / Method: batch mode / Details: PEG 4000, Sodium chloride |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: May 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→56.42 Å / Num. obs: 4958 / % possible obs: 96.8 % / Redundancy: 4.5 % / Net I/σ(I): 6.9 |
-Processing
Software |
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Refinement | Resolution: 2.424→30.746 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.424→30.746 Å
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Refine LS restraints |
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LS refinement shell |
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