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Yorodumi- PDB-6f1p: Tetragonal Lysozyme crystallized at 298 K and pH 4.5 with phospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f1p | |||||||||
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Title | Tetragonal Lysozyme crystallized at 298 K and pH 4.5 with phosphate bound | |||||||||
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 / molecular replacement / Resolution: 1.12 Å | |||||||||
Authors | Camara-Artigas, A. | |||||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding. Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f1p.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1p.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 6f1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1p ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1p | HTTPS FTP |
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-Related structure data
Related structure data | 6f1lC 6f1mC 6f1oC 6f1rC 6f9xC 6f9yC 6f9zC 6fa0C 4e3uS S: Starting model for refinement 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 | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 1.99 Å3/Da / Density % sol: 38.13 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.2 M Sodium Chloride, 0.1 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2017 | ||||||||||||||||||||||||
Radiation | Monochromator: CHANNEL-CUT MONOCHROMATOR AND A KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.12→19.19 Å / Num. obs: 44928 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.022 / Rrim(I) all: 0.073 / Net I/σ(I): 15.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E3U Resolution: 1.12→18.689 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0.33 / Phase error: 17.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.59 Å2 / Biso mean: 20.6024 Å2 / Biso min: 11.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.12→18.689 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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