[English] 日本語
Yorodumi- PDB-2gyd: Complex of equine apoferritin with the H-diaziflurane photolabeli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gyd | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of equine apoferritin with the H-diaziflurane photolabeling reagent | ||||||
Components | ferritin L subunit | ||||||
Keywords | METAL BINDING PROTEIN / helical bundles / anesthetic / isoflurane | ||||||
Function / homology | Function and homology information intracellular ferritin complex / 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 / FOURIER SYNTHESIS / Resolution: 1.72 Å | ||||||
Authors | Loll, P.J. / Rossi, M.J. / Eckenhoff, R. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2006 Title: Photoactive analogues of the haloether anesthetics provide high-resolution features from low-affinity interactions. Authors: Xi, J. / Liu, R. / Rossi, M.J. / Yang, J. / Loll, P.J. / Dailey, W.P. / Eckenhoff, R.G. | ||||||
History |
| ||||||
Remark 600 | HETEROGEN SER 27 reacts with H-diaziflurane to form the adduct 2-(1,1-DIFLUOROETHOXY)-1,1,1- ...HETEROGEN SER 27 reacts with H-diaziflurane to form the adduct 2-(1,1-DIFLUOROETHOXY)-1,1,1-TRIFLUOROETHANE (Ligand Code DFE) |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2gyd.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2gyd.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 2gyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/2gyd ftp://data.pdbj.org/pub/pdb/validation_reports/gy/2gyd | HTTPS FTP |
---|
-Related structure data
Related structure data | 1xz1S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | Biological unit is a 24-mer; see 1XZ1 for transformations required to create the 24-mer. |
-Components
#1: Protein | Mass: 19402.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: horse spleen ferritin / Source: (natural) Equus caballus (horse) / References: GenBank: 62896483, UniProt: P02791*PLUS | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-DFE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M cadmium sulfate, 0.1 M HEPES, and 1.0 M sodium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→37.13 Å / Num. all: 27676 / Num. obs: 27676 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.94 % / Rmerge(I) obs: 0.075 / Χ2: 0.69 / Net I/σ(I): 16.9 / Scaling rejects: 29232 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1XZ1 Resolution: 1.72→37.13 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.617 / SU ML: 0.054 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.533 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→37.13 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
|