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Yorodumi- PDB-9b7c: high-resolution ambient temperature structure of lysozyme soaked ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b7c | ||||||||||||
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Title | high-resolution ambient temperature structure of lysozyme soaked with sodium iodide | ||||||||||||
Components | Lysozyme C | ||||||||||||
Keywords | HYDROLASE / lysozyme | ||||||||||||
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 / SAD / Resolution: 1.1 Å | ||||||||||||
Authors | Wang, H.K. / Greisman, J.B. / Hekstra, D.R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Bayesian Priors for Comparative Crystallography Authors: Hekstra, D.R. / Wang, H.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9b7c.cif.gz | 101 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b7c.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 9b7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b7c_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9b7c_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9b7c_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 9b7c_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/9b7c ftp://data.pdbj.org/pub/pdb/validation_reports/b7/9b7c | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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) / References: UniProt: P00698, lysozyme | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PEG4000, sodium citrate, 100 mM sodium iodide, glycerol |
-Data collection
Diffraction | Mean temperature: 295 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.03752 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03752 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→79.41 Å / Num. obs: 85383 / % possible obs: 91.3 % / Redundancy: 123.4 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.005 / Rrim(I) all: 0.06 / Χ2: 0.95 / Net I/σ(I): 53.6 |
Reflection shell | Resolution: 1.1→1.12 Å / % possible obs: 22.3 % / Redundancy: 18.1 % / Rmerge(I) obs: 2.278 / Num. measured all: 9534 / Num. unique obs: 526 / CC1/2: 0.44 / Rpim(I) all: 0.527 / Rrim(I) all: 2.344 / Χ2: 0.85 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.1→56.15 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.17 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→56.15 Å
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Refine LS restraints |
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LS refinement shell |
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