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- PDB-1bwj: THE 1.8 A STRUCTURE OF MICROGRAVITY GROWN TETRAGONAL HEN EGG WHIT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bwj | ||||||
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Title | THE 1.8 A STRUCTURE OF MICROGRAVITY GROWN TETRAGONAL HEN EGG WHITE LYSOZYME | ||||||
![]() | PROTEIN (LYSOZYME) | ||||||
![]() | HYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE C | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, J. / Boggon, T.J. / Chayen, N.E. / Raftery, J. / Bi, R.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bvxC ![]() 1bwhC ![]() 1bwiC ![]() 193lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microgravity experiment / pH: 4.7 Details: CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S LIFE AND MICROGRAVITY SPACELAB (LMS) MISSION ...Details: CRYSTALLISATION TOOK PLACE IN THE EUROPEAN SPACE AGENCY (ESA) ADVANCED PROTEIN CRYSTALLISATION FACILITY (APCF) ONBOARD THE NASA SPACE SHUTTLE'S LIFE AND MICROGRAVITY SPACELAB (LMS) MISSION (STS-78). A SOLUTION OF 21 MG OF HEN EGG WHITE LYSOZYME (3 X CRYSTALLIZED, DIALYSED AND LYOPHILIZED POWDER OF CHICKEN EGG WHITE LYSOZYME SUPPLIED BY SIGMA, L-6876 BATCH NUMBER, LOT 53H7145) DISSOLVED IN 250 UL 0.04 M ACETATE BUFFER (PH 4.7) WAS USED TO FILL THE PROTEIN CHAMBER (188 UL). THE SALT CHAMBERS (541 UL) WERE FILLED WITH 1.35 M NACL AND THE BUFFER CHAMBER (59 UL) WITH 0.04 M ACETATE BUFFER (PH 4.7). SODIUM AZIDE WAS ALSO ADDED TO THE PROTEIN AND BUFFER SOLUTION AS AN ANTI-FUNGAL AGENT (1.92 MG PER 188 UL). CRYSTALLISATION TOOK PLACE AT 20+/-0.1 C., microgravity experiment, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: liquid-liquid dialysis / Details: microgravity | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
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: 0.7107 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→99 Å / Num. obs: 11846 / % possible obs: 85.5 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Rsym value: 0.075 / Net I/σ(I): 19.8 |
Reflection | *PLUS Num. measured all: 57479 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å / % possible obs: 45.1 % / Rmerge(I) obs: 0.393 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 22.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.7 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: 0.231 / Rfactor obs: 0.277 |