+Open data
-Basic information
Entry | Database: PDB / ID: 2f4a | ||||||
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Title | Triclinic cross-linked lysozyme soaked with thiourea 1.5M | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / DENATURATION / LYSOZYME / BARNASE / CROSS-LINKED CRYSTALS / GLUTARALDEHYDE / UREA / THIOUREA / BROMOETHANOL | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å | ||||||
Authors | Prange, T. / Salem, M. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f4a.cif.gz | 40.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f4a.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 2f4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f4a_validation.pdf.gz | 462 KB | Display | wwPDB validaton report |
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Full document | 2f4a_full_validation.pdf.gz | 462.6 KB | Display | |
Data in XML | 2f4a_validation.xml.gz | 8 KB | Display | |
Data in CIF | 2f4a_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/2f4a ftp://data.pdbj.org/pub/pdb/validation_reports/f4/2f4a | HTTPS FTP |
-Related structure data
Related structure data | 2f2nSC 2f30C 2f4gC 2f4yC 2f56C 2f5mC 2f5wC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: EGG / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.9 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: SODIUM NITRATE AS CRYSTALLIZING AGENT CROSS-LINKED BY VAPOR DIFFUSION WITH GLUTARALDEHYDE, PROTIEN CONCENTRATION 20 MG/ML, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.964 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 13, 2002 / Details: SI(111) CURVATED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 1.949→18.3 Å / Num. all: 7080 / Num. obs: 6985 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 |
Reflection shell | Resolution: 1.949→2.1 Å / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 6.9 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2F2N Resolution: 1.95→10 Å / Num. parameters: 4389 / Num. restraintsaints: 4186 / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1097 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0 / Rfactor Rfree error: _ / Num. reflection Rfree: _ / Total num. of bins used: 5
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