+Open data
-Basic information
Entry | Database: PDB / ID: 8gmw | ||||||||||||
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Title | Crystal structure of lysozyme | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Nam, K.H. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: To Be Published Title: Crystal structure of lysozyme Authors: Nam, K.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gmw.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmw.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gmw_validation.pdf.gz | 424.6 KB | Display | wwPDB validaton report |
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Full document | 8gmw_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 8gmw_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 8gmw_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmw ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmw | HTTPS FTP |
-Related structure data
Related structure data | 5k2kC 5k2pC 8gmvC 7wucS 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-NA / | ||||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 4.6 / Details: Na-acetate, NaCl, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→20 Å / Num. obs: 25439 / % possible obs: 96.6 % / Redundancy: 9.4 % / CC1/2: 0.995 / Net I/σ(I): 30.59 |
Reflection shell | Resolution: 1.35→1.37 Å / Num. unique obs: 1164 / CC1/2: 0.647 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WUC Resolution: 1.35→19.15 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.67 / Stereochemistry target values: ML
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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 max: 45.76 Å2 / Biso mean: 16.3882 Å2 / Biso min: 7.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→19.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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