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Yorodumi- PDB-3rft: Crystal structure of uronate dehydrogenase from Agrobacterium tum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rft | ||||||
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Title | Crystal structure of uronate dehydrogenase from Agrobacterium tumefaciens | ||||||
Components | Uronate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / apoenzyme / Rossmann Fold / NAD binding | ||||||
Function / homology | Function and homology information uronate dehydrogenase / uronate dehydrogenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.9 Å | ||||||
Authors | Parkkinen, T. / Rouvinen, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Crystal Structure of Uronate Dehydrogenase from Agrobacterium tumefaciens. Authors: Parkkinen, T. / Boer, H. / Janis, J. / Andberg, M. / Penttila, M. / Koivula, A. / Rouvinen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rft.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rft.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rft_validation.pdf.gz | 443.5 KB | Display | wwPDB validaton report |
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Full document | 3rft_full_validation.pdf.gz | 446.2 KB | Display | |
Data in XML | 3rft_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 3rft_validation.cif.gz | 56.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/3rft ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rft | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29278.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / ATCC 33970 / Gene: udh, AGR_L_3333, Atu3143 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q7CRQ0, uronate dehydrogenase #2: Chemical | ChemComp-SO4 / #3: 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: 3.89 Å3/Da / Density % sol: 68.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.8 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 208962 / Num. obs: 208931 / % possible obs: 100 % |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.81 / Num. unique all: 15436 / Rsym value: 0.329 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→47.565 Å / SU ML: 0.18 / σ(F): 1.39 / Phase error: 15.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.351 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→47.565 Å
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Refine LS restraints |
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LS refinement shell |
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