+Open data
-Basic information
Entry | Database: PDB / ID: 1tuv | ||||||
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Title | Crystal structure of YgiN in complex with menadione | ||||||
Components | Protein ygiN | ||||||
Keywords | UNKNOWN FUNCTION / menadione oxidase / monooxygenase / co-crystal with natural product / ferredoxin fold | ||||||
Function / homology | Function and homology information response to acidic pH / Oxidoreductases / catalytic activity / oxidoreductase activity / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / direct input of native model / Resolution: 1.7 Å | ||||||
Authors | Adams, M.A. / Jia, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural and Biochemical Evidence for an Enzymatic Quinone Redox Cycle in Escherichia coli: IDENTIFICATION OF A NOVEL QUINOL MONOOXYGENASE Authors: Adams, M.A. / Jia, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tuv.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tuv.ent.gz | 26.5 KB | Display | PDB format |
PDBx/mmJSON format | 1tuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tuv_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 1tuv_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 1tuv_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1tuv_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tuv ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tuv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12775.716 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygiN / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40718, UniProt: P0ADU2*PLUS |
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#2: Chemical | ChemComp-VK3 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium sulfate, sodium/potassium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2004 |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. all: 19783 / Num. obs: 19783 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 50 |
Reflection shell | Resolution: 1.69→1.77 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: direct input of native model / Resolution: 1.7→25.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.913 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.097 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.765 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→25.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20 /
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