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Yorodumi- PDB-2yyt: Crystal structure of uncharacterized conserved protein from Geoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yyt | ||||||
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Title | Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / TIM barrel / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kanagawa, M. / Baba, S. / Nakamura, Y. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of uncharacterized conserved protein from Geobacillus kaustophilus Authors: Kanagawa, M. / Baba, S. / Nakamura, Y. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yyt.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yyt.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 2yyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/2yyt ftp://data.pdbj.org/pub/pdb/validation_reports/yy/2yyt | HTTPS FTP |
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-Related structure data
-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: 26982.936 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X References: UniProt: Q5L0U0, orotidine-5'-phosphate decarboxylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.17 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium Sulfate decahydrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 7, 2006 |
Radiation | Monochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 141451 / % possible obs: 100 % / Redundancy: 2.7 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.062 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 451132.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0211 Å2 / ksol: 0.36303 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 20.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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