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Open data
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Basic information
Entry | Database: PDB / ID: 2f2n | ||||||
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Title | Triclinic hen egg lysozyme cross-linked by glutaraldehyde | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / denaturation / lysozyme / barnase / cross-linked-crystals / urea / thiourea / bromoethanol | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Prange, T. / Salem, M. / Mauguen, Y. | ||||||
![]() | ![]() Title: On the edge of the denaturation process: Application of X-ray diffraction to barnase and lysozyme cross-linked crystals with denaturants in molar concentrations. Authors: Salem, M. / Mauguen, Y. / Prange, 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 | ![]() | 43 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.5 KB | Display | ![]() |
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Full document | ![]() | 429.5 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f30C ![]() 2f4aC ![]() 2f4gC ![]() 2f4yC ![]() 2f56C ![]() 2f5mC ![]() 2f5wC ![]() 1lksS ![]() 3lztS 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: eggs / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.01 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium nitrate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Monochromator: SI(III) CURVATED MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.974 Å / Relative weight: 1 |
Reflection | Resolution: 1.603→8.7 Å / Num. all: 12253 / Num. obs: 12315 / % possible obs: 93.55 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.043 / Net I/σ(I): 32.01 |
Reflection shell | Resolution: 1.603→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 17.2 / Rsym value: 0.168 / % possible all: 87.84 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LZT, 1LKS Resolution: 1.603→8 Å / Num. parameters: 4727 / Num. restraintsaints: 4203 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 954 / Occupancy sum non hydrogen: 1179 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.603→8 Å
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Refine LS restraints |
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LS refinement shell |
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