[English] 日本語
Yorodumi- PDB-2q53: Ensemble refinement of the crystal structure of uncharacterized p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q53 | ||||||
---|---|---|---|---|---|---|---|
Title | Ensemble refinement of the crystal structure of uncharacterized protein loc79017 from Homo sapiens | ||||||
Components | Uncharacterized protein C7orf24 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information gamma-glutamylcyclotransferase / gamma-glutamylcyclotransferase activity / Glutathione synthesis and recycling / release of cytochrome c from mitochondria / protein homodimerization activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 2.01 Å | ||||||
Authors | Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of Homo sapiens protein LOC79017. Authors: Bae, E. / Bingman, C.A. / Aceti, D.J. / Phillips Jr., G.N. #1: Journal: Structure / Year: 2007 Title: Ensemble refinement of protein crystal structures: validation and application. Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2q53.cif.gz | 274.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2q53.ent.gz | 228 KB | Display | PDB format |
PDBx/mmJSON format | 2q53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q53_validation.pdf.gz | 501.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2q53_full_validation.pdf.gz | 529.1 KB | Display | |
Data in XML | 2q53_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 2q53_validation.cif.gz | 71.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/2q53 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q53 | HTTPS FTP |
-Related structure data
Related structure data | 2i5tSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Number of models | 4 |
-Components
#1: Protein | Mass: 21173.152 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C7orf24 / Plasmid: PVP30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) pRARE2 / References: UniProt: O75223 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 42.5 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2I5T. |
---|
-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Re-refinement using ensemble model Starting model: PDB entry 2I5T Resolution: 2.01→44.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1668254.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: maximum likelihood using amplitudes Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2i5t and the first data set in the deposited structure factor file for 2i5t ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2i5t and the first data set in the deposited structure factor file for 2i5t along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 4 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.199 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→44.99 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|