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Yorodumi- PDB-1bwi: THE 1.8 A STRUCTURE OF MICROBATCH OIL DROP GROWN TETRAGONAL HEN E... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bwi | ||||||
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Title | THE 1.8 A STRUCTURE OF MICROBATCH OIL DROP GROWN TETRAGONAL HEN EGG WHITE LYSOZYME | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE C | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Dong, J. / Boggon, T.J. / Chayen, N.E. / Raftery, J. / Bi, R.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 A resolution. Authors: Dong, J. / Boggon, T.J. / Chayen, N.E. / Raftery, J. / Bi, R.C. / Helliwell, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bwi.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bwi.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 1bwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bwi ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bwi | HTTPS FTP |
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-Related structure data
Related structure data | 1bvxC 1bwhC 1bwjC 193lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) Gallus gallus (chicken) / Cellular location: EGG WHITE / References: UniProt: P00698, lysozyme |
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#2: 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: 2.08 Å3/Da / Density % sol: 40.78 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: drop under paraffin oil / pH: 4.7 Details: A SOLUTION CONTAINING 40 MG/ML OF LYSOZYME (SIGMA L-6876, BATCH NUMBER, LOT 65H7025, IE A DIFFERENT SIGMA SAMPLE TO THE EXPERIMENTS DESCRIBED ABOVE) IN 10 MM SODIUM CITRATE BUFFER PH 4.7 WAS ...Details: A SOLUTION CONTAINING 40 MG/ML OF LYSOZYME (SIGMA L-6876, BATCH NUMBER, LOT 65H7025, IE A DIFFERENT SIGMA SAMPLE TO THE EXPERIMENTS DESCRIBED ABOVE) IN 10 MM SODIUM CITRATE BUFFER PH 4.7 WAS MIXED IN AN EPPENDORF TUBE WITH EQUAL VOLUMES OF 12 % SODIUM CHLORIDE (BDH). THE MIXTURE WAS FILTERED THROUGH A 0.22 UM FILTER AND 8 UL DROPS WERE MANUALLY DISPENSED UNDER PARAFFIN OIL USING A GILSON MICRO PIPPETTE. OVER 20 IDENTICAL DROPS WERE SET UP AND, WITHIN A WEEK, SINGLE CRYSTALS TYPICALLY MEASURING 0.5 X 0.4 X 0.3 MM WERE OBTAINED IN MOST OF THE DROPS. CRYSTALLISATION TOOK PLACE AT A TEMPERATURE OF 18 - 20 C., drops under paraffin oil, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: microbatch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→99 Å / Num. obs: 12081 / % possible obs: 85.5 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.077 / Rsym value: 0.08 / Net I/σ(I): 22.6 |
Reflection | *PLUS % possible obs: 87.2 % / Num. measured all: 73591 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å / % possible obs: 43.2 % / Rmerge(I) obs: 0.151 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.8→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.329 / Rfactor obs: 0.259 |