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- PDB-2q3s: Ensemble refinement of the protein crystal structure of gene prod... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2q3s | ||||||
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Title | Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g06450 | ||||||
![]() | Protein At5g06450 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ensemble Refinement / Refinement Methodology Development / Protein / homohexamer / At5g06450 / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | ![]() exoribonuclease II / exoribonuclease II activity / RISC complex binding / plant-type vacuole / single-stranded DNA 3'-5' DNA exonuclease activity / regulatory ncRNA-mediated gene silencing / positive regulation of miRNA metabolic process / : / nucleic acid binding / nucleus / cytoplasm Similarity search - Function | ||||||
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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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 918.4 KB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 448.3 KB | Display | |
Data in CIF | ![]() | 633.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2q3mC ![]() 2q3oC ![]() 2q3pC ![]() 2q3qC ![]() 2q3rC ![]() 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 ![]() 2q52C ![]() 1vk0S 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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Unit cell |
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Number of models | 8 |
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Components
#1: Protein | Mass: 23243.074 Da / Num. of mol.: 6 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: 2.8 Å3/Da / Density % sol: 56.04 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1VK0. |
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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
Software |
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Refinement | Method to determine structure: Re-refinement using ensemble model Starting model: PDB entry 1VK0 Resolution: 2.1→34.88 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3994599 / 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 1vk0 and the first data set in the deposited structure factor file for 1vk0 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1vk0 and the first data set in the deposited structure factor file for 1vk0 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: 50.315 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→34.88 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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