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- PDB-2q4x: 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: 2q4x | ||||||
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Title | Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990 | ||||||
![]() | Seed maturation protein PM36 homolog | ||||||
![]() | PLANT PROTEIN / Ensemble Refinement / Refinement Methodology Development / TENA_THI-4 DOMAIN / TENA/THI-4/PQQC FAMILY / AT3G16990 / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | ![]() aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / cytosol 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. #1: ![]() Title: Crystal structure of gene locus At3g16990 from Arabidopsis thaliana Authors: Blommel, P.G. / Smith, D.W. / Bingman, C.A. / Dyer, D.H. / Rayment, I. / Holden, H.M. / Fox, B.G. / Phillips Jr., G.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 712.1 KB | Display | ![]() |
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PDB format | ![]() | 611.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 649.4 KB | Display | ![]() |
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Full document | ![]() | 916.6 KB | Display | |
Data in XML | ![]() | 202.6 KB | Display | |
Data in CIF | ![]() | 287.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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 ![]() 2q4yC ![]() 2q4zC ![]() 2q50C ![]() 2q51C ![]() 2q52C ![]() 2f2gS 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 |
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Components
#1: Protein | Mass: 25332.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.5 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2F2G. |
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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 2F2G Resolution: 2.1→28.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2683790.75 / 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 2f2g and the first data set in the deposited structure factor file for 2f2g ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2f2g and the first data set in the deposited structure factor file for 2f2g 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: 64.319 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→28.04 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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