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Open data
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Basic information
Entry | Database: PDB / ID: 4h8z | ||||||
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Title | Radiation damage study of lysozyme - 0.21 MGy | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Sutton, K.A. / Snell, E.H. | ||||||
![]() | ![]() Title: Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies. Authors: Sutton, K.A. / Black, P.J. / Mercer, K.R. / Garman, E.F. / Owen, R.L. / Snell, E.H. / Bernhard, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.8 KB | Display | ![]() |
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PDB format | ![]() | 27.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h8xC ![]() 4h8yC ![]() 4h90C ![]() 4h91C ![]() 4h92C ![]() 4h93C ![]() 4h94C ![]() 4h9aC ![]() 4h9bC ![]() 4h9cC ![]() 4h9eC ![]() 4h9fC ![]() 4h9hC ![]() 4h9iC ![]() 6lyzS 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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Unit cell |
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Components on special symmetry positions |
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Details | biological unit is the same as asym. |
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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 | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 7.5% sodium chloride, 100 mM sodium acetate pH 4.8, 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2011 / Details: mirrors |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.1998→50 Å / Num. all: 36830 / Num. obs: 36830 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5.36 / Redundancy: 4.5 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.029 / Net I/σ(I): 43.2 |
Reflection shell | Resolution: 1.1998→1.2323 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 22.95 / Rsym value: 0.076 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 6LYZ Resolution: 1.1998→26.909 Å / Occupancy max: 1 / Occupancy min: 0.41 / FOM work R set: 0.8793 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 18.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.088 Å2 / ksol: 0.436 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 40.78 Å2 / Biso mean: 13.1438 Å2 / Biso min: 6.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.137 Å / Luzzati sigma a obs: 0.044 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1998→26.909 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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