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Yorodumi- PDB-4xsm: Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xsm | ||||||
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Title | Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with D-talitol | ||||||
Components | D-tagatose 3-epimerase | ||||||
Keywords | ISOMERASE / Epimerase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas cichorii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yoshida, H. / Yoshihara, A. / Ishii, T. / Izumori, K. / Kamitori, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Appl. Microbiol. Biotechnol. / Year: 2016 Title: X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates Authors: Yoshida, H. / Yoshihara, A. / Ishii, T. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xsm.cif.gz | 243.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xsm.ent.gz | 194.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xsm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xsm_validation.pdf.gz | 490.7 KB | Display | wwPDB validaton report |
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Full document | 4xsm_full_validation.pdf.gz | 527 KB | Display | |
Data in XML | 4xsm_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 4xsm_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/4xsm ftp://data.pdbj.org/pub/pdb/validation_reports/xs/4xsm | HTTPS FTP |
-Related structure data
Related structure data | 4xslC 4ytqC 4ytrC 4ytsC 4yttC 4ytuC 5j8lC 2qulS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33858.613 Da / Num. of mol.: 4 / Mutation: C66S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas cichorii (bacteria) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: O50580, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-TLZ / #4: 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: 2.41 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 6-9% PEG4000, 0.1M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 5, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→25.68 Å / Num. obs: 54404 / % possible obs: 96.7 % / Redundancy: 1.94 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.19 / Χ2: 1 / Net I/σ(I): 2.7 / Num. measured all: 106443 / Scaling rejects: 799 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QUL Resolution: 2.3→25.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3245721 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.6172 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.86 Å2 / Biso mean: 36.1 Å2 / Biso min: 10.52 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 2.3→25.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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