+Open data
-Basic information
Entry | Database: PDB / ID: 1bb3 | ||||||
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Title | HUMAN LYSOZYME MUTANT A96L | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / LYSOZYME / GLYCOSIDASE | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Headley, A.G. / Roe, S.M. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bb3.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bb3.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/1bb3 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/1bb3 | HTTPS FTP |
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-Related structure data
Related structure data | 1lz1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14762.773 Da / Num. of mol.: 2 / Mutation: A96L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P61626, lysozyme #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.18 % |
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Crystal grow | pH: 4.5 / Details: pH 4.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: X-RAY RESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→30 Å / Num. obs: 30141 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.79→1.82 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.026 / Mean I/σ(I) obs: 2.7 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ1 Resolution: 1.8→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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