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Yorodumi- PDB-4ytr: Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ytr | ||||||
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Title | Crystal structure of D-tagatose 3-epimerase C66S from Pseudomonas cichorii in complex with 1-deoxy L-tagatose | ||||||
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: 1.9 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. #1: Journal: J.MOL.BIOL. / Year: 2007 Title: Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose. Authors: Yoshida, H. / Yamada, M. / Nishitani, T. / Takada, G. / 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 | 4ytr.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ytr.ent.gz | 211.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ytr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ytr_validation.pdf.gz | 502 KB | Display | wwPDB validaton report |
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Full document | 4ytr_full_validation.pdf.gz | 517.4 KB | Display | |
Data in XML | 4ytr_validation.xml.gz | 55.8 KB | Display | |
Data in CIF | 4ytr_validation.cif.gz | 82.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/4ytr ftp://data.pdbj.org/pub/pdb/validation_reports/yt/4ytr | HTTPS FTP |
-Related structure data
Related structure data | 4xslC 4xsmC 4ytqC 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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1 |
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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: Sugar | ChemComp-TGK / #4: Chemical | ChemComp-TGJ / | #5: 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: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 6-9 % PEG4000, 0.1 M 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: Oct 23, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→22.14 Å / Num. obs: 92108 / % possible obs: 98.2 % / Redundancy: 2.92 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1 / Net I/σ(I): 8.7 / Num. measured all: 271251 / Scaling rejects: 2036 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.9→21.71 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1909410 / 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: 64.5925 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.31 Å2 / Biso mean: 21 Å2 / Biso min: 6.47 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 1.9→21.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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