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Yorodumi- PDB-7xf8: Crystal Structure of Human Lysozyme Complexed with N-Acetyl-alpha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xf8 | ||||||||||||
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Title | Crystal Structure of Human Lysozyme Complexed with N-Acetyl-alpha-D-Glucosamine | ||||||||||||
Components | Lysozyme C | ||||||||||||
Keywords | HYDROLASE / lysozyme / human / N-Acetyl-alpha-D-Glucosamine / N-Acetyl-D-Glucosamine / NAG / NDG | ||||||||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Nam, K.H. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Appl Sci (Basel) / Year: 2022 Title: Crystal Structure of Human Lysozyme Complexed with N-Acetyl-alpha-d-glucosamine. 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 | 7xf8.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xf8.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 7xf8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xf8_validation.pdf.gz | 712.9 KB | Display | wwPDB validaton report |
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Full document | 7xf8_full_validation.pdf.gz | 713.3 KB | Display | |
Data in XML | 7xf8_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 7xf8_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/7xf8 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/7xf8 | HTTPS FTP |
-Related structure data
Related structure data | 7xf6C 7xf7C 7e02S 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
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LYZ, LZM / Production host: Oryza sativa (Asian cultivated rice) / References: UniProt: P61626, lysozyme |
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#2: Sugar | ChemComp-NDG / |
#3: 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: 1.7 Å3/Da / Density % sol: 27.68 % |
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Crystal grow | Temperature: 277.5 K / Method: batch mode / Details: Na-acetate, PEG 6K, NaCl |
-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: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 15319 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.993 / Net I/σ(I): 27.59 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 688 / CC1/2: 0.832 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 700 / Resolution: 1.6→30.47 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.8 / 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: 53.98 Å2 / Biso mean: 20.7198 Å2 / Biso min: 2.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→30.47 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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