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Open data
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Basic information
Entry | Database: PDB / ID: 5b1f | ||||||
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Title | Crystal structure of hen egg-white lysozyme | ||||||
![]() | Lysozyme C | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugahara, M. / Suzuki, M. / Nango, E. | ||||||
![]() | ![]() Title: Crystal structure of hen egg-white lysozyme Authors: Sugahara, M. / Suzuki, M. / Nango, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.5 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3wunC ![]() 4ym8C ![]() 5b1gC ![]() 3wulS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.69 % |
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Crystal grow![]() | Temperature: 293 K / Method: batch mode / Details: NaCl |
-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Feb 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→30 Å / Num. obs: 5727 / % possible obs: 100 % / Redundancy: 453 % / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Mean I/σ(I) obs: 10.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3WUL Resolution: 2.3→25.014 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→25.014 Å
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Refine LS restraints |
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LS refinement shell |
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