+Open data
-Basic information
Entry | Database: PDB / ID: 8dcw | |||||||||||||||
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Title | Lysozyme cluster 0062 (NAG and benzamidine ligands) | |||||||||||||||
Components | Lysozyme C | |||||||||||||||
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: 2 Å | |||||||||||||||
Authors | Soares, A.S. / Yamada, Y. / Jakoncic, J. / Schneider, D.K. / Bernstein, H.J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Serial crystallography with multi-stage merging of thousands of images. Authors: Soares, A.S. / Yamada, Y. / Jakoncic, J. / McSweeney, S. / Sweet, R.M. / Skinner, J. / Foadi, J. / Fuchs, M.R. / Schneider, D.K. / Shi, W. / Andi, B. / Andrews, L.C. / Bernstein, H.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dcw.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dcw.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dcw_validation.pdf.gz | 1016.1 KB | Display | wwPDB validaton report |
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Full document | 8dcw_full_validation.pdf.gz | 1022.6 KB | Display | |
Data in XML | 8dcw_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 8dcw_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/8dcw ftp://data.pdbj.org/pub/pdb/validation_reports/dc/8dcw | HTTPS FTP |
-Related structure data
Related structure data | 8dctC 8dcuC 8dcvC 4n8zS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Sugars , 2 types, 2 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) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#5: Sugar | ChemComp-NDG / |
-Non-polymers , 4 types, 217 molecules
#2: Chemical | ChemComp-NA / | ||||
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#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-BEN / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 4% SODIUM CHLORIDE, 100MM SODIUM ACETATE PH 4.6, 120MG/ML |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 14987 / % possible obs: 97.9 % / Redundancy: 5.08 % / CC1/2: 0.859 / Rmerge(I) obs: 0.408 / Net I/σ(I): 3.73 |
Reflection shell | Resolution: 2→2.12 Å / Rmerge(I) obs: 1.47 / Num. unique obs: 2411 / CC1/2: 0.254 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N8Z Resolution: 2→39.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.647 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.413 Å2
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Refinement step | Cycle: 1 / Resolution: 2→39.42 Å
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Refine LS restraints |
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