+Open data
-Basic information
Entry | Database: PDB / ID: 1vat | ||||||
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Title | Iodine derivative of hen egg-white lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Iodine-derivative / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Takeda, K. / Miyatake, H. / Park, S.Y. / Kawamoto, M. / Kamiya, N. / Miki, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 2004 Title: Multi-wavelength anomalous diffraction method for I and Xe atoms using ultra-high-energy X-rays from SPring-8 Authors: Takeda, K. / Miyatake, H. / Park, S.Y. / Kawamoto, M. / Kamiya, N. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vat.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vat.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1vat.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/1vat ftp://data.pdbj.org/pub/pdb/validation_reports/va/1vat | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-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) / Tissue: hen egg-white / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 50mg/ml HEWL, 20%(w/v) PEG4000, 100mM sodium citrate (pH 5.5), 100mM sodium iodide, and 20%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.5400, 0.3746, 0.3734 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 26, 2001 | ||||||||||||
Radiation | Monochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→25 Å / Num. all: 15776 / Num. obs: 15776 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 32.2 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 1539 / Rsym value: 0.212 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 16.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.019
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