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- PDB-2q52: Ensemble refinement of the crystal structure of a glycolipid tran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2q52 | ||||||
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Title | Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria | ||||||
![]() | Glycolipid transfer-like protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / GLTP superfamily / GLTP-like / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
![]() | ![]() Title: Ensemble refinement of protein crystal structures: validation and application. Authors: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 664.2 KB | Display | ![]() |
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PDB format | ![]() | 579.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2q3mC ![]() 2q3oC ![]() 2q3pC ![]() 2q3qC ![]() 2q3rC ![]() 2q3sC ![]() 2q3tC ![]() 2q3uC ![]() 2q3vC ![]() 2q3wC ![]() 2q40C ![]() 2q41C ![]() 2q42C ![]() 2q43C ![]() 2q44C ![]() 2q45C ![]() 2q46C ![]() 2q47C ![]() 2q48C ![]() 2q49C ![]() 2q4aC ![]() 2q4bC ![]() 2q4cC ![]() 2q4dC ![]() 2q4eC ![]() 2q4fC ![]() 2q4hC ![]() 2q4iC ![]() 2q4jC ![]() 2q4kC ![]() 2q4lC ![]() 2q4mC ![]() 2q4nC ![]() 2q4oC ![]() 2q4pC ![]() 2q4qC ![]() 2q4rC ![]() 2q4sC ![]() 2q4tC ![]() 2q4uC ![]() 2q4vC ![]() 2q4xC ![]() 2q4yC ![]() 2q4zC ![]() 2q50C ![]() 2q51C ![]() 2i3fS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Number of models | 8 | |||||||||||||||||||||||||||
Components on special symmetry positions |
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Components
#1: Protein | Mass: 25868.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.6 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2I3F. |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
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Processing
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Refinement | Method to determine structure: Re-refinement using ensemble model Starting model: PDB entry 2I3F Resolution: 1.38→41.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2180669.5 / 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 2i3f and the first data set in the deposited structure factor file for 2i3f ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2i3f and the first data set in the deposited structure factor file for 2i3f along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 8 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.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.95 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.38→41.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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