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Yorodumi- PDB-2bpu: The Kedge Holmium Derivative of Hen Egg-White Lysozyme at high re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bpu | ||||||
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Title | The Kedge Holmium Derivative of Hen Egg-White Lysozyme at high resolution from Single Wavelength Anomalous Diffraction | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / HOLMIUM / KEDGE / ULTRA HIGH ENERGY / HIGH RESOLUTION / COMPTON / EXPERIMENTAL PHASES / ALLERGEN / HYDROLASE BACTERIOLYTIC ENZYME / GLYCOSIDASE / SAD | ||||||
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 / SAD / Resolution: 1.35 Å | ||||||
Authors | Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2006 Title: Anomalous Diffraction at Ultra-High Energy for Protein Crystallography. Authors: Jakoncic, J. / Di Michiel, M. / Zhong, Z. / Honkimaki, V. / Jouanneau, Y. / Stojanoff, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bpu.cif.gz | 66.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bpu.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 2bpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bpu ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpu | 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
#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 | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: 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: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | pH: 4.5 / Details: pH 4.50 |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.2229 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.2229 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. obs: 49334 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 2.2 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→27.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.927 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06 Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED LOOPS WERE MANUALLY CONSTRUCTED. 124 (TOTAL RESIDUES 129) WERE AUTOMATICALLY CONSTRUCTED WITH ARP.
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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: 12.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→27.83 Å
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Refine LS restraints |
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