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Yorodumi- PDB-3uxi: Crystal structure of L-rhamnose isomerase W38A mutant from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uxi | ||||||
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Title | Crystal structure of L-rhamnose isomerase W38A mutant from Bacillus halodurans | ||||||
Components | L-Rhamnose isomerase | ||||||
Keywords | ISOMERASE / (beta/alpha)8 barrel domain | ||||||
Function / homology | Function and homology information L-rhamnose isomerase / L-rhamnose isomerase activity / rhamnose catabolic process / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus halodurans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å | ||||||
Authors | Doan, T.T.N. / Prabhu, P. / Kim, J.K. / Jeya, M. / Kang, L.W. / Lee, J.K. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structure-based studies on the metal binding of two-metal-dependent sugar isomerases. Authors: Prabhu, P. / Doan, T.N. / Tiwari, M. / Singh, R. / Kim, S.C. / Hong, M.K. / Kang, Y.C. / Kang, L.W. / Lee, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uxi.cif.gz | 326.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uxi.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uxi_validation.pdf.gz | 460.7 KB | Display | wwPDB validaton report |
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Full document | 3uxi_full_validation.pdf.gz | 503 KB | Display | |
Data in XML | 3uxi_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 3uxi_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/3uxi ftp://data.pdbj.org/pub/pdb/validation_reports/ux/3uxi | 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
#1: Protein | Mass: 48960.570 Da / Num. of mol.: 4 / Mutation: W38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: rhaA, BH1552 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KCL9, L-rhamnose isomerase #2: Chemical | ChemComp-MN / | #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: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / pH: 6.5 Details: 10% (w/v) PEG 8000, 0.1M HEPES pH 6.0, 0.2M sodium acetate, VAPOR DIFFUSION, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.73→50 Å / Num. obs: 90338 / % possible obs: 79 % |
Reflection shell | Resolution: 2.75→2.8 Å / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→45.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.346 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.425 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.506 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→45.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.731→2.801 Å / Total num. of bins used: 20
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