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Yorodumi- PDB-4wm3: High pressure protein crystallography of hen egg white lysozyme a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wm3 | ||||||
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Title | High pressure protein crystallography of hen egg white lysozyme at 710 MPa | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Yamada, H. / Nagae, T. / Watanabe, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: High-pressure protein crystallography of hen egg-white lysozyme Authors: Yamada, H. / Nagae, T. / Watanabe, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wm3.cif.gz | 39.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wm3.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 4wm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/4wm3 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/4wm3 | HTTPS FTP |
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-Related structure data
Related structure data | 4wldC 4wltC 4wlxC 4wlyC 4wm1C 4wm2C 4wm4C 4wm5C 4wm6C 4xenC C: citing same article (ref.) |
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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 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.47 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / Details: Sodium chloride |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.71 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 16944 / % possible obs: 99.4 % / Redundancy: 6.7 % / Net I/σ(I): 48.9 |
-Processing
Software | Name: REFMAC / Version: 5.7.0032 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→33.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.1 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.111 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.831 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→33.91 Å
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Refine LS restraints |
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