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Yorodumi- PDB-3rfv: Crystal structure of Uronate dehydrogenase from Agrobacterium tum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rfv | ||||||
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Title | Crystal structure of Uronate dehydrogenase from Agrobacterium tumefaciens complexed with NADH and product | ||||||
Components | Uronate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ternary complex / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 3rfv.cif.gz | 183.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rfv.ent.gz | 146.8 KB | Display | PDB format |
PDBx/mmJSON format | 3rfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rfv_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3rfv_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 3rfv_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 3rfv_validation.cif.gz | 58.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/3rfv ftp://data.pdbj.org/pub/pdb/validation_reports/rf/3rfv | HTTPS FTP |
-Related structure data
Related structure data | 3rftSC 3rfxC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 | #3: Sugar | #4: Chemical | ChemComp-PO4 / #5: 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: 3.9 Å3/Da / Density % sol: 68.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 2.5 Details: 1.8 M ammonium phosphate, Tris-HCl, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 81720 / Num. obs: 81563 / % possible obs: 99.8 % |
Reflection shell | Resolution: 2.1→2.12 Å / Redundancy: 11 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 6.8 / Num. unique all: 5946 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RFT Resolution: 2.1→19.758 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 17.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.804 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.758 Å
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Refine LS restraints |
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LS refinement shell |
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