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Yorodumi- PDB-4b4i: 1.20 A Structure of Lysozyme Crystallized with (S)-2-methyl-2,4- ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b4i | ||||||
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Title | 1.20 A Structure of Lysozyme Crystallized with (S)-2-methyl-2,4- pentanediol | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / CHIRALITY | ||||||
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: 1.2 Å | ||||||
Authors | Jakoncic, J. / Berger, J. / Stauber, M. / Axelbaum, A. / Asherie, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Crystallization of Lysozyme with (R)-, (S)- and (Rs)-2-Methyl-2,4-Pentanediol Authors: Stauber, M. / Jakoncic, J. / Berger, J. / Karp, J.M. / Axelbaum, A. / Sastow, D. / Buldyrev, S.V. / Hrnjez, B.J. / Asherie, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b4i.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b4i.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 4b4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b4i ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b4i | 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 | #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: 2.03 Å3/Da / Density % sol: 39.4 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: CRYSTALLIZATION BY HANGING DROP AT 4C. CONDITIONS IN DROP: PROTEIN AT 35 MG/ML IN 200MM TRIS (PH=8.0) AND 30% (V/V) (S)-MPD. CONDITIONS IN RESERVOIR: 200MM TRIS (PH=8.0) AND 60% (V/V) (S)-MPD. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.8856 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 23, 2011 / Details: TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 36597 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 14 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 45.1 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE MODEL Resolution: 1.2→21.48 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.061 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY
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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: 17.107 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→21.48 Å
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