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Yorodumi- PDB-2q3m: Ensemble refinement of the protein crystal structure of an Arabid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q3m | ||||||
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Title | Ensemble refinement of the protein crystal structure of an Arabidopsis thaliana putative steroid sulphotransferase | ||||||
Components | Flavonol sulfotransferase-like | ||||||
Keywords | TRANSFERASE / Ensemble Refinement / Refinement Methodology Development / Steroid Sulphotransferase / Apo / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
Function / homology | Function and homology information brassinosteroid metabolic process / brassinosteroid sulfotransferase activity / flavonoid sulfotransferase activity / Transferases; Transferring sulfur-containing groups; Sulfotransferases / response to salicylic acid / sulfation / sulfotransferase activity / response to salt stress / defense response / Golgi apparatus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / Re-refinement using ensemble model / Resolution: 1.9 Å | ||||||
Authors | Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | 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, G.N. #1: Journal: Proteins / Year: 2004 Title: Crystal structure of At2g03760, a putative steroid sulfotransferase from Arabidopsis thaliana Authors: Smith, D.W. / Johnson, K.A. / Bingman, C.A. / Aceti, D.J. / Blommel, P.G. / Wrobel, R.L. / Frederick, R.O. / Zhao, Q. / Sreenath, H. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Newman, C.S. / ...Authors: Smith, D.W. / Johnson, K.A. / Bingman, C.A. / Aceti, D.J. / Blommel, P.G. / Wrobel, R.L. / Frederick, R.O. / Zhao, Q. / Sreenath, H. / Fox, B.G. / Volkman, B.F. / Jeon, W.B. / Newman, C.S. / Ulrich, E.L. / Hegeman, A.D. / Kimball, T. / Thao, S. / Sussman, M.R. / Markley, J.L. / Phillips Jr., G.N. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q3m.cif.gz | 913.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q3m.ent.gz | 794.5 KB | Display | PDB format |
PDBx/mmJSON format | 2q3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q3m_validation.pdf.gz | 551.2 KB | Display | wwPDB validaton report |
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Full document | 2q3m_full_validation.pdf.gz | 617 KB | Display | |
Data in XML | 2q3m_validation.xml.gz | 188.9 KB | Display | |
Data in CIF | 2q3m_validation.cif.gz | 256.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/2q3m ftp://data.pdbj.org/pub/pdb/validation_reports/q3/2q3m | HTTPS FTP |
-Related structure data
Related structure data | 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 2q52C 1q44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Number of models | 16 |
-Components
#1: Protein | Mass: 37184.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: apo form / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At2g03760, F19B11.21 / Plasmid: PVP13 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: P52839, Transferases; Transferring sulfur-containing groups; Sulfotransferases |
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#2: Chemical | ChemComp-MLA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.2 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1Q44. |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: Re-refinement using ensemble model Starting model: PDB entry 1Q44 Resolution: 1.9→19.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2625918.25 / 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 1q44 and the first data set in the deposited structure factor file for 1q44 ...Details: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 1q44 and the first data set in the deposited structure factor file for 1q44 along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 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: 58.125 Å2 / ksol: 0.384 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.79 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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