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Yorodumi- PDB-3nkl: Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nkl | ||||||
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Title | Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri | ||||||
Components | UDP-D-quinovosamine 4-dehydrogenase | ||||||
Keywords | oxidoreductase/lyase / alpha-beta fold / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / oxidoreductase-lyase complex | ||||||
Function / homology | Function and homology information Lyases; Carbon-oxygen lyases; Hydro-lyases / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / membrane => GO:0016020 / oxidoreductase activity / lyase activity Similarity search - Function | ||||||
Biological species | Vibrio fischeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Kim, Y. / Mack, J. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2010 Title: Crystal Structure of UDP-D-Quinovosamine 4-Dehydrogenase from Vibrio fischeri Authors: Kim, Y. / Mack, J. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nkl.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nkl.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkl ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkl | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15762.071 Da / Num. of mol.: 2 / Fragment: residues 144-281 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_0197 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q5E8F4, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, Lyases; Carbon-oxygen lyases; Hydro-lyases |
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-Non-polymers , 5 types, 253 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-ACY / | #5: Chemical | ChemComp-CL / | #6: 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: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25 %w/v Polyehtlyene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 25582 / Num. obs: 25582 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 24.67 Å2 / Rsym value: 0.051 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.26 / Num. unique all: 832 / Rsym value: 0.341 / % possible all: 62.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→42.217 Å / SU ML: 0.24 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.645 Å2 / ksol: 0.358 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.217 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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