+Open data
-Basic information
Entry | Database: PDB / ID: 1gwd | ||||||
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Title | Tri-iodide derivative of hen egg-white lysozyme | ||||||
Components | LYSOZYME C | ||||||
Keywords | LYSOZYME / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME / ALLER | ||||||
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 / OTHER / Resolution: 1.77 Å | ||||||
Authors | Evans, G. / Bricogne, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Triiodide Derivatization and Combinatorial Counter-Ion Replacement: Two Methods for Enhancing Phasing Signal Using Laboratory Cu Kalpha X-Ray Equipment Authors: Evans, G. / Bricogne, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gwd.cif.gz | 40 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gwd.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 1gwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gwd_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 1gwd_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 1gwd_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1gwd_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/1gwd ftp://data.pdbj.org/pub/pdb/validation_reports/gw/1gwd | HTTPS FTP |
-Related structure data
-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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 6 types, 121 molecules
#2: Chemical | ChemComp-IOD / #3: Chemical | #4: Chemical | ChemComp-CMO / | #5: Chemical | ChemComp-CL / #6: Chemical | #7: 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: 2.08 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: 2M NACL, 0.025M SODIUM ACETATE AT PH4.7,0.1% SODIUM AZIDE, 25% ETHYLENE GLYCOL AND THEN SOAKED IN AN EQUIVALENT SOLUTION WITH 50MM KI/50MM I2., pH 4.70 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 4.7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: SUPPER MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→15.091 Å / Num. obs: 143946 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 12.1 % / Rmerge(I) obs: 0.021 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.046 / Mean I/σ(I) obs: 15.5 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 15.09 Å |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.77→15.09 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION APPLIED
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Refinement step | Cycle: LAST / Resolution: 1.77→15.09 Å
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Refinement | *PLUS Rfactor obs: 0.17 / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.172 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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