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Yorodumi- PDB-1q44: Crystal Structure of an Arabidopsis Thaliana Putative Steroid Sul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q44 | ||||||
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Title | Crystal Structure of an Arabidopsis Thaliana Putative Steroid Sulfotransferase | ||||||
Components | Steroid Sulfotransferase | ||||||
Keywords | TRANSFERASE / Arabidopsis Thaliana / Steroid Sulfotransferase / Apo / Structural Genomics / Protein Structure Initiative / 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 / sulfotransferase activity / response to salt stress / defense response / Golgi apparatus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Phillips Jr., G.N. / Smith, D.W. / Johnson, K.A. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q44.cif.gz | 75.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q44.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 1q44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q44 ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q44 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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) / Gene: At2g03760 / 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 / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.2 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: microbatch / pH: 6 Details: Sodium Malonate, MES, pH 6.0, Micro-Batch, temperature 297K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24 ℃ / Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003 / Details: Bent cylindrical Si-mirror (Rh coating) | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.9→50 Å / Num. all: 32697 / Num. obs: 32697 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 43.02 | ||||||||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 5.07 / Num. unique all: 3191 / Rsym value: 0.336 / % possible all: 98.8 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 25 Å | ||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 1.95 Å / % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: built from MAD Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.9 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.419 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.947 Å / Total num. of bins used: 20
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Refinement | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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