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Yorodumi- PDB-2htx: Crystal Structure Analysis of Hen Egg White Lysozyme Crosslinked ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2htx | ||||||
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Title | Crystal Structure Analysis of Hen Egg White Lysozyme Crosslinked by Polymerized Glutaraldehyde in Acidic Environment | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Tetragonal / Crosslinked / Glutaraldehyde | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.56 Å | ||||||
Authors | Wine, Y. / Cohen-Hadar, N. / Freeman, A. / Lagziel-Simis, S. / Frolow, F. | ||||||
Citation | Journal: Biotechnol.Bioeng. / Year: 2007 Title: Elucidation of the mechanism and end products of glutaraldehyde crosslinking reaction by X-ray structure analysis Authors: Wine, Y. / Cohen-Hadar, N. / Freeman, A. / Frolow, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2htx.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2htx.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 2htx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/2htx ftp://data.pdbj.org/pub/pdb/validation_reports/ht/2htx | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: see REMARK 400 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 125 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-220 / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | COMPOUND UNDER ACIDIC CONDITIONS TWO LYSINE RESIDUES FROM NEIGHBORING LYSOZYME MOLECULES REACT WITH ...COMPOUND UNDER ACIDIC CONDITIONS |
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-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 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M Sodium Acetate, 7% NaCl, 25% Ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 15, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→55.73 Å / Num. all: 17157 / Num. obs: 17157 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 47.2 |
Reflection shell | Resolution: 1.56→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.34 / Rsym value: 0.367 / % possible all: 87.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: In-House Coordinates Resolution: 1.56→55.73 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.035 / SU ML: 0.05 Isotropic thermal model: Structure was refined using Anisotropic thermal parameters Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.082 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.913 Å2
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Refine analyze | Luzzati coordinate error obs: 0.049 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→55.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 Å / Total num. of bins used: 20
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