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Yorodumi- PDB-6kcd: Room temperature structure of lysozyme delivered in shortening B ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kcd | ||||||
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Title | Room temperature structure of lysozyme delivered in shortening B by serial millisecond crystallography | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / room temperature / serial crystallography / lysozyme | ||||||
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: 1.5 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Sci Rep / Year: 2020 Title: Shortening injection matrix for serial crystallography. Authors: 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 | 6kcd.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcd.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 6kcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcd ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcd | HTTPS FTP |
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-Related structure data
Related structure data | 6kcaC 6kcbC 6kccC 6ig6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1582295 / 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 | ChemComp-NA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.12 % |
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Crystal grow | Temperature: 293.5 K / Method: small tubes / pH: 4.5 / Details: sodium acetate, PEG 8000, NaCl |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→80 Å / Num. obs: 20406 / % possible obs: 100 % / Redundancy: 756.6 % / Biso Wilson estimate: 35.87 Å2 / CC1/2: 0.9936 / R split: 0.0658 / Net I/σ(I): 9.27 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 285.8 % / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1995 / CC1/2: 0.5183 / R split: 0.7095 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IG6 Resolution: 1.5→55.989 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.93 Å2 / Biso mean: 40.5869 Å2 / Biso min: 29.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→55.989 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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