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- PDB-2d4i: Monoclinic hen egg-white lysozyme crystallized at pH4.5 form heav... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d4i | ||||||
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Title | Monoclinic hen egg-white lysozyme crystallized at pH4.5 form heavy water solution | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / phase transition / rigid-body motion / TLS analysis | ||||||
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 | ![]() ![]() | ||||||
![]() | Harata, K. / Akiba, T. | ||||||
![]() | ![]() Title: Structural phase transition of monoclinic crystals of hen egg-white lysozyme Authors: Harata, K. / Akiba, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.6 KB | Display | ![]() |
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PDB format | ![]() | 100 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2d4jC ![]() 2d4kC ![]() 1lj4S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-DOD / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.68 % |
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Crystal grow | Temperature: 298 K / Method: batch method / pH: 4.5 Details: 1% protein, 2% sodium nitrate, D2O solution with pD 4.5 adjusted with 1M acetic acid, batch method, temperature 298K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 7, 2004 / Details: Conforcal Max-Flux optics |
Radiation | Monochromator: curved mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→17.2 Å / Num. all: 77767 / Num. obs: 68963 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.39 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 1.13→1.17 Å / Rmerge(I) obs: 0.415 / % possible all: 57.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LJ4 Resolution: 1.16→17.2 Å / σ(F): 0 / Stereochemistry target values: SHELX97 default Details: The author asigned the Rfree reflections by the following SHELXL97 input command line L.S. 5 -20 which indicates 5 cycles of least-squares calculation and ignore every 20th reflections (5%) ...Details: The author asigned the Rfree reflections by the following SHELXL97 input command line L.S. 5 -20 which indicates 5 cycles of least-squares calculation and ignore every 20th reflections (5%) in the refinement for the Rfree calculation
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Refinement step | Cycle: LAST / Resolution: 1.16→17.2 Å
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LS refinement shell | Resolution: 1.13→1.22 Å / Rfactor Rwork: 0.376 |