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Open data
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Basic information
Entry | Database: PDB / ID: 7fcw | ||||||
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Title | X-ray structure of H2O-solvent lysozyme | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / hydrolase H2O solution | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chatake, T. / Tanaka, I. / Kusaka, K. / Fujiwara, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Protonation states of hen egg-white lysozyme observed using D/H contrast neutron crystallography. Authors: Chatake, T. / Tanaka, I. / Kusaka, K. / Fujiwara, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.7 KB | Display | ![]() |
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PDB format | ![]() | 27.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fcuSC ![]() 7veiC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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) ![]() ![]() |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.5 Details: 15-25mg/mL HEWL, 50mM sodium acetate (pH4.5), 0.1g/mL NiCl2 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→37.82 Å / Num. obs: 22878 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.017 / Rrim(I) all: 0.065 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.43→1.45 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.676 / Num. unique obs: 1136 / CC1/2: 0.915 / Rpim(I) all: 0.182 / Rrim(I) all: 0.701 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7FCU Resolution: 1.43→35.43 Å / SU ML: 0.1414 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.7491 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: 24.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.43→35.43 Å
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Refine LS restraints |
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LS refinement shell |
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