+Open data
-Basic information
Entry | Database: PDB / ID: 2xth | ||||||
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Title | K2PtBr6 binding to lysozyme | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / CRYO-TEMPERATURE / HEAVY ATOM DERIVATIVE | ||||||
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 / OTHER / Resolution: 1.8 Å | ||||||
Authors | Helliwell, J.R. / Bell, A.M.T. / Bryant, P. / Fisher, S. / Habash, J. / Helliwell, M. / Margiolaki, I. / Kaenket, S. / Watier, Y. / Wright, J. / Yalamanchili, S.K. | ||||||
Citation | Journal: Z.Kristallogr. / Year: 2010 Title: Time-Dependent Analysis of K2Ptbr6 Binding to Lysozyme Studied by Protein Powder and Single Crystal X-Ray Analysis Authors: Helliwell, J.R. / Bell, A.M.T. / Bryant, P. / Fisher, S. / Habash, J. / Helliwell, M. / Margiolaki, I. / Kaenket, S. / Watier, Y. / Wright, J. / Yalamanchili, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xth.cif.gz | 41.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xth.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/2xth ftp://data.pdbj.org/pub/pdb/validation_reports/xt/2xth | 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 / Details: K2PTBR6 BOUND / Source: (natural) GALLUS GALLUS (chicken) / Tissue: EGG WHITE AND POLYMORPHONUCLEAR LEUKOCYTES / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | #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: 1.94 Å3/Da / Density % sol: 36.69 % / Description: NONE |
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Crystal grow | pH: 4.7 Details: 10% SODIUM CHLORIDE W/V; PH 4.7 0.04M SODIUM ACETATE BUFFER; 80MG OF LYSOZYME PROTEIN 2ML AQUEOUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Dec 9, 2008 / Details: OSMIC CONFOCAL MAX-FLUX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→55.6 Å / Num. obs: 12866 / % possible obs: 87.2 % / Observed criterion σ(I): 1 / Redundancy: 6.17 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 2.2 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 1.89 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 23.2 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.8→55.64 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.573 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / 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: 17.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→55.64 Å
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