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Yorodumi- PDB-4e3u: Crystal Structure of Hen Egg White Lysozyme Cryoprotected in Proline -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e3u | ||||||
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Title | Crystal Structure of Hen Egg White Lysozyme Cryoprotected in Proline | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Tanner, J.J. / Pemberton, T.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Proline: Mother Nature's cryoprotectant applied to protein crystallography. Authors: Pemberton, T.A. / Still, B.R. / Christensen, E.M. / Singh, H. / Srivastava, D. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e3u.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e3u.ent.gz | 45.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/4e3u ftp://data.pdbj.org/pub/pdb/validation_reports/e3/4e3u | HTTPS FTP |
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-Related structure data
Related structure data | 4e3vC 4e3wC 4e3xC 2lyzS C: citing same article (ref.) S: Starting model for refinement |
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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 / Details: Egg White / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-PRO / | ||
#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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 1.0M sodium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 123 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→19.499 Å / Num. all: 19076 / Num. obs: 19076 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rsym value: 0.028 / Net I/σ(I): 46.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2LYZ Resolution: 1.5→19.499 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8454 / SU ML: 0.21 / σ(F): 0 / Phase error: 21.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.412 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.34 Å2 / Biso mean: 17.3662 Å2 / Biso min: 8.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.499 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -0.994 Å / Origin y: 19.9158 Å / Origin z: 19.313 Å
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Refinement TLS group | Selection details: Chain A |