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Yorodumi- PDB-1qio: SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE CAUSED BY INTENSE SYNCHRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qio | ||||||
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Title | SPECIFIC CHEMICAL AND STRUCTURAL DAMAGE CAUSED BY INTENSE SYNCHROTRON RADIATION TO HEN EGG WHITE LYSOZYME | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / RADIATION DAMAGES / DISULFIDE BOND / HYDROLASE (O-GLYCOSYL) | ||||||
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 / OTHER / Resolution: 1.2 Å | ||||||
Authors | Kryger, G. / Weik, M. / Ravelli, R.B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Specific chemical and structural damage to proteins produced by synchrotron radiation. Authors: Weik, M. / Ravelli, R.B. / Kryger, G. / McSweeney, S. / Raves, M.L. / Harel, M. / Gros, P. / Silman, I. / Kroon, J. / Sussman, J.L. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Thermal Expansion of Hen-Egg-White Lysozyme. Comparison of the 1.9 Angstroms Resolution Structures of the Tetragonal Form of the Enzyme at 100K and 298K Authors: Young, A.C. / Tilton, R.F. / Dewan, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qio.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qio.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qio ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qio | HTTPS FTP |
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-Related structure data
Related structure data | 1qidC 1qieC 1qifC 1qigC 1qihC 1qiiC 1qijC 1qikC 1qimC 194lS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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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) / Cellular location: EGG WHITE / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: 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: 1.65 Å3/Da / Density % sol: 25.3 % Description: DATA COMPLETE TO 1.4 ANG. DATA BETWEEN 1.4 AND 1.2ANG WERE COLLECTED IN THE CORNERS OF THE SQUARE DETECTOR. | ||||||||||||||||||
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Crystal grow | pH: 4.7 Details: CRYSTALLIZED FROM 2-6% NACL, 0.2 M SODIUM ACETATE PH 4.7. | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9315 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 1999 / Details: BENT TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9315 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→25 Å / Num. obs: 34095 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4.11 % / Rsym value: 0.061 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.89 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.176 / % possible all: 69.2 |
Reflection | *PLUS Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 69.2 % / Rmerge(I) obs: 0.176 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 194L Resolution: 1.2→20 Å / Num. parameters: 10637 / Num. restraintsaints: 12618 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1170.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.141 / Rfactor Rfree: 0.187 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.9 Å2 | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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