+Open data
-Basic information
Entry | Database: PDB / ID: 2ybh | ||||||
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Title | Nitrate X-ray induced reduction on HEWL crystals (2.31 MGy). | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / NITRATE REDUCTION | ||||||
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: 2 Å | ||||||
Authors | De la Mora, E. / Carmichael, I. / Garman, E.F. | ||||||
Citation | Journal: J.Synchrotron.Radiat. / Year: 2011 Title: Effective Scavenging at Cryotemperatures: Further Increasing the Dose Tolerance of Protein Crystals. Authors: De La Mora, E. / Carmichael, I. / Garman, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ybh.cif.gz | 44.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ybh.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ybh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybh ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybh | HTTPS FTP |
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-Related structure data
Related structure data | 2ybiC 2ybjC 2yblC 2ybmC 2ybnC 2ydgC 2w1lS 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) / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NO3 / #3: 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 Å3/Da / Density % sol: 38.62 % / Description: NONE |
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Crystal grow | pH: 4.7 / Details: 200 MM SODIUM ACETATE BUFFER PH 4.7, 10% W/V NACL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: EMG-T5 KOHZU DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 2→35 Å / Num. obs: 8348 / % possible obs: 99.4 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Biso Wilson estimate: 12.786 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 8.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W1L Resolution: 2→35 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.083 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.025 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35 Å
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Refine LS restraints |
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