+
Open data
-
Basic information
Entry | Database: PDB / ID: 3np0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Pd(allyl)/apo-E45C/H49A/R52H-rHLFr | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Ueno, T. / Abe, S. / Takezawa, Y. / Aoyagi, H. / Hikage, T. / Watanabe, Y. / Kitagawa, S. | ||||||
![]() | ![]() Title: Definite coordination arrangement of organometallic palladium complexes accumulated on the designed interior surface of apo-ferritin. Authors: Wang, Z. / Takezawa, Y. / Aoyagi, H. / Abe, S. / Hikage, T. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 469.1 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nozC ![]() 3np2C ![]() 1datS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 24|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 19760.340 Da / Num. of mol.: 1 / Mutation: E45C, H49A, R52H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 228 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PLL / #4: Chemical | ChemComp-CD / | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.62 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2009 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. obs: 41911 / % possible obs: 98.3 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.286 / % possible all: 88.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.48→19.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.945 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.578 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→19.29 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.481→1.52 Å / Total num. of bins used: 20
|