+Open data
-Basic information
Entry | Database: PDB / ID: 6msx | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Iron containing ferritin at 1.43A | |||||||||
Components | Ferritin light chain | |||||||||
Keywords | METAL TRANSPORT / nucleation / ferritin / drug discovery | |||||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å | |||||||||
Authors | Blackburn, A. / Partowmah, S.H. / Brennan, H.M. / Mestizo, K.E. / Stivala, C.D. / Petreczky, J. / Perez, A. / Horn, A. / McSweeney, S. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: To Be Published Title: A simple technique to improve microcrystals using gel exclusion of nucleation inducing elements Authors: Blackburn, A. / Partowmah, S.H. / Brennan, H.M. / Mestizo, K.E. / Stivala, C.D. / Petreczky, J. / Perez, A. / Horn, A. / McSweeney, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6msx.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6msx.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 6msx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/6msx ftp://data.pdbj.org/pub/pdb/validation_reports/ms/6msx | HTTPS FTP |
---|
-Related structure data
Related structure data | 6mx9C 1ierS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 / Fragment: residue 2-175 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791 |
---|
-Non-polymers , 5 types, 259 molecules
#2: Chemical | ChemComp-SO4 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | ChemComp-CD / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: A 20 uL pellet of 50 mM cadmium sulfate in 2% agar was deposited on a cover slip. Adjacent to this was positioned ferritin (10 ul of 50 mg/ml ferritin, Sigma F4503) and precipitant (10 ul of ...Details: A 20 uL pellet of 50 mM cadmium sulfate in 2% agar was deposited on a cover slip. Adjacent to this was positioned ferritin (10 ul of 50 mg/ml ferritin, Sigma F4503) and precipitant (10 ul of 3.5M Ammonium Sulfate and 100 mM Tris pH 7.4). The cover slip was equilibrated over 3.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 10, 2018 |
Radiation | Monochromator: 13.4737 KeV / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. obs: 45041 / % possible obs: 99.14 % / Redundancy: 138.2 % / Net I/σ(I): 31.81 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 48.9 % / Num. unique obs: 3445 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IER Resolution: 1.43→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.909 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.055 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.43→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|