[English] 日本語
Yorodumi- PDB-5fst: Structure of lysozyme prepared by the 'soak-and-freeze' method un... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fst | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of lysozyme prepared by the 'soak-and-freeze' method under 100 bar of krypton pressure | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / MURAMIDASE / LYSOZYME / KRYPTON / PRESSURE / FLASH FREEZING | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 | Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2016 Title: Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology. Authors: Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fst.cif.gz | 99 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fst.ent.gz | 77.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/5fst ftp://data.pdbj.org/pub/pdb/validation_reports/fs/5fst | HTTPS FTP |
---|
-Related structure data
Related structure data | 5frcC 5fsjC 5fspC 5fssC 1lz8S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-KR / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41 % / Description: ANOMALOUS DATA |
---|---|
Crystal grow | pH: 4.8 Details: 10% (W/V) NACL, 0.1M NA ACETATE PH 4.8 25% (V/V) ETH-GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.864 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.864 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→55.86 Å / Num. obs: 70048 / % possible obs: 99.9 % / Observed criterion σ(I): 4.65 / Redundancy: 13.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.2→1.27 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.65 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ8 Resolution: 1.2→55.86 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED NOT REFINED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 16.126 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→55.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|