+Open data
-Basic information
Entry | Database: PDB / ID: 7bmq | ||||||
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Title | HEWL in cesium chloride (1.71 M CsCl in cryo protectant) | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / Cesium / Phasing | ||||||
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 / SAD / Resolution: 1.79 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 | 7bmq.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bmq.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bmq_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 7bmq_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 7bmq_validation.xml.gz | 9 KB | Display | |
Data in CIF | 7bmq_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/7bmq ftp://data.pdbj.org/pub/pdb/validation_reports/bm/7bmq | HTTPS FTP |
-Related structure data
Related structure data | 7bmoC 7bmpC 7bmrC 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 | ChemComp-EDO / | #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: 1.99 Å3/Da / Density % sol: 38.23 % |
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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: 1.79→39.38 Å / Num. obs: 11383 / % possible obs: 98.7 % / Redundancy: 19.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.023 / Rrim(I) all: 0.106 / Net I/σ(I): 24.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→39.38 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.257 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / 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: 74.01 Å2 / Biso mean: 18.518 Å2 / Biso min: 8.18 Å2
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Refinement step | Cycle: final / Resolution: 1.79→39.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→39.38 Å
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