+Open data
-Basic information
Entry | Database: PDB / ID: 8b3u | ||||||
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Title | Hen Egg White Lysozyme 6s in situ crystallization | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Henkel, A. / Galchenkova, M. / Yefanov, O. / Hakanpaeae, J. / Chapman, H.N. / Oberthuer, D. | ||||||
Funding support | 1items
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Citation | Journal: Iucrj / Year: 2023 Title: JINXED: just in time crystallization for easy structure determination of biological macromolecules. Authors: Henkel, A. / Galchenkova, M. / Maracke, J. / Yefanov, O. / Klopprogge, B. / Hakanpaa, J. / Mesters, J.R. / Chapman, H.N. / Oberthuer, D. #1: Journal: Biorxiv / Year: 2022 Title: JINXED: Just in time crystallization for easy structure determination of biological macromolecules Authors: Henkel, A. / Galchenkova, M. / Maracke, J. / Yefanov, O. / Hakanpaa, J. / Mesters, J.R. / Chapman, H.N. / Oberthur, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3u.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3u.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 8b3u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b3u_validation.pdf.gz | 443.6 KB | Display | wwPDB validaton report |
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Full document | 8b3u_full_validation.pdf.gz | 444.6 KB | Display | |
Data in XML | 8b3u_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 8b3u_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3u ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3u | HTTPS FTP |
-Related structure data
Related structure data | 8b3lC 8b3tC 8b3vC 6ftrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Gallus gallus (chicken) / References: UniProt: P00698 |
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-Non-polymers , 5 types, 82 molecules
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.53 % |
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Crystal grow | Temperature: 293 K / Method: microfluidic Details: 0.1 M sodium acetate, pH 4.6, 2.7 M NaCl, 15 % PEG4000, 6 % ethylene glycol |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→39.6 Å / Num. obs: 13615 / % possible obs: 100 % / Redundancy: 502 % / Biso Wilson estimate: 21.01 Å2 / CC1/2: 0.989 / CC star: 0.997 / R split: 0.1167 / Net I/σ(I): 10.21 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 25.6 % / Num. unique obs: 674 / CC1/2: 0.247 / CC star: 0.63 / R split: 1.71 / % possible all: 100 |
Serial crystallography sample delivery | Description: CFEL TapeDrive 2.0 / Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FTR Resolution: 1.71→39.6 Å / SU ML: 0.2227 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9088 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→39.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.751151091168 Å / Origin y: 99.8970778597 Å / Origin z: 9.0916501634 Å
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Refinement TLS group | Selection details: all |