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Yorodumi- PDB-6jxp: Room temperature structure of lysozyme delivered in LCP by serial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jxp | ||||||
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Title | Room temperature structure of lysozyme delivered in LCP by serial millisecond crystallography | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / serial crystallography / LCP | ||||||
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 / Resolution: 1.56 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: J.Synchrotron Radiat. / Year: 2019 Title: Sample delivery using viscous media, a syringe and a syringe pump for serial crystallography. Authors: Park, S.Y. / Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jxp.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jxp.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jxp ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jxp | HTTPS FTP |
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-Related structure data
Related structure data | 6jxqC 6irjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1562532 / Data set type: diffraction image 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: 16257.660 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: 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: 1.79 Å3/Da / Density % sol: 31.4 % |
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Crystal grow | Temperature: 293.5 K / Method: small tubes / Details: sodium acetate, PEG 8000, NaCl |
-Data collection
Diffraction | Mean temperature: 298.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→78.7 Å / Num. obs: 17418 / % possible obs: 99.93 % / Redundancy: 318.4 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.991 / R split: 0.0987 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.56→1.61 Å / Mean I/σ(I) obs: 1.26 / Num. unique obs: 1685 / CC1/2: 0.436 / R split: 0.8866 / % possible all: 99.23 |
Serial crystallography sample delivery | Method: injection |
Serial crystallography data reduction | Crystal hits: 24258 / Frames indexed: 19411 / Frames total: 40000 / Lattices indexed: 19411 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IRJ Resolution: 1.56→55.44 Å / SU ML: 0.1805 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.7775
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→55.44 Å
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Refine LS restraints |
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LS refinement shell |
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