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Yorodumi- PDB-7bmr: HEWL in cesium chloride (0.25 M CsCl in protein buffer and 1.71 M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bmr | ||||||
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Title | HEWL in cesium chloride (0.25 M CsCl in protein buffer and 1.71 M CsCl in cryo protectant) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Cesium / Phasing | ||||||
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 / SAD / Resolution: 1.78 Å | ||||||
Authors | Koelmel, W. / Kuper, J. / Kisker, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Sci Rep / Year: 2021 Title: Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem. Authors: Koelmel, W. / Kuper, J. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bmr.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bmr.ent.gz | 31.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/7bmr ftp://data.pdbj.org/pub/pdb/validation_reports/bm/7bmr | HTTPS FTP |
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-Related structure data
Related structure data | 7bmoC 7bmpC 7bmqC 7bmsC 7bmtC 7bmuC 7bmvC 7bmwC 7bmxC 7bmyC 7bmzC 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 / 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: Chemical | ChemComp-CS / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 38.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 50 mM sodium acetate pH 4.5, 1.71 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.7712 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→39.48 Å / Num. obs: 11475 / % possible obs: 98.9 % / Redundancy: 19.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.033 / Rrim(I) all: 0.156 / Net I/σ(I): 18.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→39.48 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.536 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.56 Å2 / Biso mean: 17.969 Å2 / Biso min: 5.56 Å2
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Refinement step | Cycle: final / Resolution: 1.78→39.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.784→1.831 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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