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Yorodumi- PDB-6vlo: X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vlo | ||||||
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Title | X-ray Structure of the R141 Sugar 4,6-dehydratase from Acanthamoeba polyphaga Minivirus | ||||||
Components | Putative dTDP-D-glucose 4,6-dehydratase | ||||||
Keywords | OXIDOREDUCTASE / Acanthamoeba polyphaga minivirus / dehydratase / dideoxysugar / UDP-viosamine | ||||||
Function / homology | Function and homology information dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process Similarity search - Function | ||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Thoden, J.B. / Ferek, J.D. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2020 Title: Biochemical analysis of a sugar 4,6-dehydratase from Acanthamoeba polyphaga Mimivirus. Authors: Ferek, J.D. / 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 | 6vlo.cif.gz | 278 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vlo.ent.gz | 222.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vlo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vlo_validation.pdf.gz | 696.2 KB | Display | wwPDB validaton report |
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Full document | 6vlo_full_validation.pdf.gz | 699.8 KB | Display | |
Data in XML | 6vlo_validation.xml.gz | 2.4 KB | Display | |
Data in CIF | 6vlo_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/6vlo ftp://data.pdbj.org/pub/pdb/validation_reports/vl/6vlo | HTTPS FTP |
-Related structure data
Related structure data | 1r66S 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: 37171.996 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5UR12, dTDP-glucose 4,6-dehydratase #2: Chemical | ChemComp-TYD / #3: Chemical | ChemComp-NAD / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 13-16% PEG-5000, 2% ethylene glycol, 100 mM HEPES, in the presence of 5 mM dTDP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 87647 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 44.5 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.298 / Num. unique obs: 4281 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R66 Resolution: 2.05→38.88 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.43 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.173 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.3 Å2 / Biso mean: 33.577 Å2 / Biso min: 16.44 Å2
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Refinement step | Cycle: final / Resolution: 2.05→38.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.101 Å / Rfactor Rfree error: 0
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