+Open data
-Basic information
Entry | Database: PDB / ID: 1k2w | ||||||
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Title | Crystal structure of sorbitol dehydrogenase from R. sphaeroides | ||||||
Components | SORBITOL DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase / enzyme | ||||||
Function / homology | Function and homology information galactitol 2-dehydrogenase / galactitol 2-dehydrogenase activity / L-iditol 2-dehydrogenase / L-iditol 2-dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Philippsen, A. / Schirmer, T. / Stetefeld, J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structure of zinc-independent sorbitol dehydrogenase from Rhodobacter sphaeroides at 2.4 A resolution. Authors: Philippsen, A. / Schirmer, T. / Stein, M.A. / Giffhorn, F. / Stetefeld, J. #1: Journal: Microbiology (Reading, Engl.) / Year: 1995 Title: Polyol metabolism of Rhodobacter sphaeroides: biochemical characterization of a short-chain sorbitol dehydrogenase Authors: Schauder, S. / Schneider, K.H. / Giffhorn, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k2w.cif.gz | 107.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2w.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 1k2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k2w_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 1k2w_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 1k2w_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 1k2w_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2w ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2w | HTTPS FTP |
-Related structure data
Related structure data | 1gegS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Details | biological assembly is dimer according to sedimentation analysis |
-Components
#1: Protein | Mass: 27040.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59787, L-iditol 2-dehydrogenase #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: 2.29 Å3/Da / Density % sol: 45.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG4000, methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 22993 / Num. obs: 21038 / % possible obs: 91.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.079 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.3→2.42 Å / % possible all: 73.3 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Highest resolution: 2.42 Å / Lowest resolution: 2.57 Å / % possible obs: 92.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1GEG Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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