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- PDB-4bad: Hen egg-white lysozyme structure in complex with the europium tri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4bad | ||||||
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Title | Hen egg-white lysozyme structure in complex with the europium tris- hydroxymethyltriazoledipicolinate complex at 1.35 A resolution. | ||||||
![]() | LYSOZYME C | ||||||
![]() | HYDROLASE / CLICK-CHEMISTRY / ANOMALOUS SCATTERING / DE NOVO PHASING / EXPERIMENTAL PHASING / LANTHANIDE COMPLEX / DIPICOLINATE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Talon, R. / Kahn, R. / Gautier, A. / Nauton, L. / Girard, E. | ||||||
![]() | ![]() Title: Clicked Europium Dipicolinate Complexes for Protein X-Ray Structure Determination. Authors: Talon, R. / Nauton, L. / Canet, J. / Kahn, R. / Girard, E. / Gautier, A. #1: ![]() Title: Protein Crystallography Through Supramolecular Interactions between a Lanthanide Complex and Arginine. Authors: Pompidor, G. / D'Aleo, A. / Vicat, J. / Toupet, L. / Giraud, N. / Kahn, R. / Maury, O. #2: ![]() Title: A Dipicolinate Lanthanide Complex for Solving Protein Structures Using Anomalous Diffraction. Authors: Pompidor, G. / Maury, O. / Vicat, J. / Kahn, R. #3: ![]() Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme. Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.3 KB | Display | ![]() |
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PDB format | ![]() | 62.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ROCHE APPLIED SCIENCE POWDER, CATALOG NUMBER 10837059001 Source: (natural) ![]() ![]() |
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-Non-polymers , 6 types, 174 molecules ![](data/chem/img/HM6.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EU3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EU3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HM6 / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE PROVIDED CORRESPOND |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 27 % / Description: NONE |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 0.1 M SODIUM ACETATE PH 4.6, 0.4-1.5 M SODIUM CHLORIDE, 0.00025 M PROTEIN, 0.0027 M LANTHANIDE COMPLEX, 293 K, 3-7 DAYS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2009 / Details: KIRKPATRICK-BAEZ BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→19.24 Å / Num. obs: 26192 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 11.16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.8 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 1.35→18.773 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 13.78 / Stereochemistry target values: ML Details: ACCORDING TO THE HIGH RESOLUTION, ANISOTROPIC ADP REFINEMENT WAS APPLIED FOR ALL ATOMS. LIGANDS OCCUPANCIES WERE FIXED ACCORDING TO THE LANTHANIDE ION OCCUPANCY
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.447 Å2 / ksol: 0.382 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→18.773 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 37.7944 Å / Origin y: 18.6379 Å / Origin z: 9.7564 Å
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Refinement TLS group | Selection details: ALL |