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Yorodumi- PDB-1xq1: X-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xq1 | ||||||
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Title | X-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS THALIANA GENE AT1G07440 | ||||||
Components | PUTATIVE TROPINONE REDUCATSE | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / CESG / AT1G07440 / REDUCTIVELY METHYLATED PROTEIN / PUTATIVE TROPINONE REDUCTASE / PSI / Center for Eukaryotic Structural Genomics | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / extracellular region Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Wesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: To be published Title: X-RAY STRUCTURE OF PUTATIVE TROPINONE REDUCATSE FROM ARABIDOPSIS THALIANA GENE AT1G07440 Authors: Center for Eukaryotic Structural Genomics | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xq1.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xq1.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 1xq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/1xq1 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/1xq1 | HTTPS FTP |
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-Related structure data
Related structure data | 1ae1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28360.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g07440 / Plasmid: pVP-13 (pQE derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) p(LacI+RARE) / References: UniProt: Q9ASX2, UniProt: P0DKI3*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 MG/ML PROTEIN, 12 PERCENT MEPEG 2000, 0.21 M AMMONIUM SULFATE, 0.10 M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: APS-1 / Detector: CCD / Date: Jul 31, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→38.3 Å / Num. all: 14486 / Num. obs: 14488 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 25.4 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 36 / Limit k min: 0 / Limit l max: 53 / Limit l min: 0 / Observed criterion F max: 117786.47 / Observed criterion F min: 0.3 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.533 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AE1 Resolution: 2.1→38.3 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 55.0751 Å2 / ksol: 0.360732 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77 Å2 / Biso mean: 36.62 Å2 / Biso min: 18.53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→38.3 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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