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Yorodumi- PDB-2o8i: Crystal structure of protein Atu2327 from Agrobacterium tumefacie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o8i | ||||||
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Title | Crystal structure of protein Atu2327 from Agrobacterium tumefaciens str. C58 | ||||||
Components | Hypothetical protein Atu2327 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Atu2327 / Agrobacterium tumefaciens str. C58 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information allantoin biosynthetic process / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / urate catabolic process / carboxy-lyase activity / purine nucleobase metabolic process Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Chang, C. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of protein Atu2327 from Agrobacterium tumefaciens str. C58 Authors: Chang, C. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o8i.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o8i.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 2o8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o8i_validation.pdf.gz | 422.1 KB | Display | wwPDB validaton report |
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Full document | 2o8i_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 2o8i_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 2o8i_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/2o8i ftp://data.pdbj.org/pub/pdb/validation_reports/o8/2o8i | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17929.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_C_4230, Atu2327 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivatives / References: UniProt: Q8UD01, UniProt: A9CI02*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 grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes pH 7.5, 1.5M Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2006 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 13337 / Num. obs: 13334 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 48.96 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 6.72 / Num. unique all: 1294 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→46.73 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.246 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.195 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.139 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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