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Yorodumi- PDB-5l9j: Room temperature X-ray diffraction of tetragonal HEWL. First data... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l9j | ||||||
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Title | Room temperature X-ray diffraction of tetragonal HEWL. First data set (0.31 MGy) | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / room temperature / radiation damage | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Castellvi, A. / Juanhuix, J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J Synchrotron Radiat / Year: 2017 Title: Uridine as a new scavenger for synchrotron-based structural biology techniques. Authors: Crosas, E. / Castellvi, A. / Crespo, I. / Fulla, D. / Gil-Ortiz, F. / Fuertes, G. / Kamma-Lorger, C.S. / Malfois, M. / Aranda, M.A. / Juanhuix, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l9j.cif.gz | 69.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5l9j.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 5l9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l9j_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 5l9j_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 5l9j_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 5l9j_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l9/5l9j ftp://data.pdbj.org/pub/pdb/validation_reports/l9/5l9j | HTTPS FTP |
-Related structure data
Related structure data | 5la5C 5la8C 5lafC 5lagC 5lanC 1bwhS 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) / Tissue: Hen egg white / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: Protein: 40-80 mg/ml of protein in 200mM NaAcetate pH 4.7 Crystallization condition: 200mM NaAcetate pH 4.7, 10% NaCl PH range: 4.7 |
-Data collection
Diffraction | Mean temperature: 298 K / Ambient temp details: Room temperature |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979268 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2015 / Details: kb mirrors |
Radiation | Monochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979268 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.62 Å / Num. obs: 19825 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 13.765 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.3 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1BWH Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.896 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.061 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.94 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→20 Å
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Refine LS restraints |
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