[English] 日本語
Yorodumi- PDB-2d3i: Crystal Structure of Aluminum-Bound Ovotransferrin at 2.15 Angstr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d3i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Aluminum-Bound Ovotransferrin at 2.15 Angstrom Resolution | ||||||
Components | Ovotransferrin | ||||||
Keywords | METAL TRANSPORT / aluminum / transferrin / Metal-binding / Transport | ||||||
Function / homology | Function and homology information extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / antibacterial humoral response / iron ion transport / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Mizutani, K. / Mikami, B. / Aibara, S. / Hirose, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of aluminium-bound ovotransferrin at 2.15 Angstroms resolution. Authors: Mizutani, K. / Mikami, B. / Aibara, S. / Hirose, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2d3i.cif.gz | 148 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2d3i.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 2d3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/2d3i ftp://data.pdbj.org/pub/pdb/validation_reports/d3/2d3i | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ovtS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 75957.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P02789 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.5 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG400, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 7, 2005 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 40672 / Num. obs: 40021 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.308 / % possible all: 94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OVT Resolution: 2.15→49.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1578922.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.0788 Å2 / ksol: 0.366437 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→49.03 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|