+Open data
-Basic information
Entry | Database: PDB / ID: 7fcu | ||||||
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Title | X-ray structure of D2O-solvent lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / hydrolase D2O solution | ||||||
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: 1.42 Å | ||||||
Authors | Chatake, T. / Tanaka, I. / Kusaka, K. / Fujiwara, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fcu.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fcu.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 7fcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/7fcu ftp://data.pdbj.org/pub/pdb/validation_reports/fc/7fcu | HTTPS FTP |
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-Related structure data
Related structure data | 7fcwC 7veiC 1ieeS 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 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 | ChemComp-NI / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DOD / |
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: 2.06 Å3/Da / Density % sol: 40.4 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
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: 1.42→39.57 Å / Num. obs: 23269 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 18.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.015 / Rrim(I) all: 0.044 / Net I/σ(I): 36.6 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 15 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1130 / CC1/2: 0.933 / Rpim(I) all: 0.171 / Rrim(I) all: 0.665 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEE Resolution: 1.42→35.39 Å / SU ML: 0.1425 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0551 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: 23.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→35.39 Å
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Refine LS restraints |
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LS refinement shell |
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