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Yorodumi- PDB-2pak: Structure of a H51N mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-keto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pak | ||||||
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Title | Structure of a H51N mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from Aneurinibacillus thermoaerophilus complexed with TDP | ||||||
Components | DTDP-6-deoxy-3,4-keto-hexulose isomerase | ||||||
Keywords | ISOMERASE / deoxysugar biosynthesis / S-Layer biosynthesis / ketoisomerase | ||||||
Function / homology | Function and homology information TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose-forming) / isomerase activity Similarity search - Function | ||||||
Biological species | Aneurinibacillus thermoaerophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Davis, M.L. / Thoden, J.B. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The X-ray Structure of dTDP-4-Keto-6-deoxy-D-glucose-3,4-ketoisomerase. Authors: Davis, M.L. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pak.cif.gz | 71.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pak.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pa/2pak ftp://data.pdbj.org/pub/pdb/validation_reports/pa/2pak | HTTPS FTP |
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-Related structure data
Related structure data | 2pa7SC 2paeC 2pamC 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
#1: Protein | Mass: 16234.509 Da / Num. of mol.: 2 / Mutation: H51N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aneurinibacillus thermoaerophilus (bacteria) Strain: L420-91T / Gene: fdtA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q6T1W8, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Chemical | #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: 2.91 Å3/Da / Density % sol: 57.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 18% PEG 3400, 150mM LiCl, 100mM CHES, 10mM TDP, 20mM fucose, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 14, 2007 / Details: Montel |
Radiation | Monochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 15617 / Num. obs: 15617 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.0959 / Rsym value: 0.0959 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.39→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1595 / Rsym value: 0.422 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2PA7 Resolution: 2.4→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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