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Yorodumi- PDB-1vdt: The crystal structure of the tetragonal form of hen egg white lys... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vdt | ||||||
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Title | The crystal structure of the tetragonal form of hen egg white lysozyme at 1.7 angstroms resolution under basic conditions in space | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / hen egg white / tetragonal / microgravity | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. | ||||||
Citation | Journal: to be published Title: The crystal structure of the tetragonal form of hen egg white lysozyme at 1.7 angstroms resolution under basic conditions in space Authors: Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. #1: Journal: Proceedings of the Twenty-Third International Symposium on Space Technology and Science Year: 2002 Title: Microgravity Influences the Nucleation Process of Protein Crystal Growth Authors: Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vdt.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vdt.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/1vdt ftp://data.pdbj.org/pub/pdb/validation_reports/vd/1vdt | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 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: 2.07 Å3/Da / Density % sol: 40.45 % |
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 14, 1998 |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55.7 Å / Num. all: 13566 / Num. obs: 13566 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 6.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→9.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 749626.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1372 Å2 / ksol: 0.309714 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→9.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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