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Yorodumi- PDB-3gnx: Structure of dehydrated D-xylose isomerase from streptomyces rubi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gnx | ||||||
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Title | Structure of dehydrated D-xylose isomerase from streptomyces rubiginosus | ||||||
Components | Xylose isomerase | ||||||
Keywords | ISOMERASE / Protein D-Xylose Isomerase Glucose Dehydrated / Carbohydrate metabolism / Cytoplasm / Magnesium / Metal-binding / Pentose shunt / Xylose metabolism | ||||||
Function / homology | Function and homology information xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces rubiginosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gramiccia, F. / Schiltz, M. | ||||||
Citation | Journal: To be Published Title: Dehydration-induced structural phase transition in crystals of D-xylose isomerase from streptomyces rubiginosus Authors: Gramiccia, F. / Besnard, C. / Schiltz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gnx.cif.gz | 167 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gnx.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gnx ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gnx | HTTPS FTP |
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-Related structure data
Related structure data | 1xigS S: Starting model for refinement |
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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: 43123.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase #2: Sugar | #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | Sequence details | THE PROTEIN USED IN THE STUDY WAS DIRECTLY EXTRACTED FROM STREPTOMYCES RUBIGINOSUS. AUTHOR BELIEVE ...THE PROTEIN USED IN THE STUDY WAS DIRECTLY EXTRACTED FROM STREPTOMYC | |
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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: 2.37 Å3/Da / Density % sol: 48.19 % |
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Crystal grow | Temperature: 278 K / pH: 7 Details: 6mM Tris-HCl, 33mg/ml crystalline suspension, 0.91M ammonium sulfate, 1mM magnesium sulfate (Hampton Research Ltd.); Soaked in xylitol solution, pH 7.0, temperature 278K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Type: OTHER |
Detector | Type: STOE / Detector: IMAGE PLATE / Date: Oct 10, 2007 / Details: Xenocs multilayer optics |
Radiation | Monochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→94.49 Å / Num. all: 51870 / Num. obs: 51870 / % possible obs: 98.3 % / Redundancy: 4 % / Biso Wilson estimate: 16.836 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XIG Resolution: 2→38.35 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.592 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.15 / 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: 14.967 Å2
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Refinement step | Cycle: LAST / Resolution: 2→38.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.004→2.056 Å / Total num. of bins used: 20
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