+Open data
-Basic information
Entry | Database: PDB / ID: 1r6y | ||||||
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Title | Crystal structure of YgiN from Escherichia coli | ||||||
Components | Protein ygiN | ||||||
Keywords | Structural genomics / Unknown function / hypothetical protein / functional annotation / ferredoxin-like fold / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
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 / MAD / Resolution: 2.2 Å | ||||||
Authors | Adams, M.A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
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 | 1r6y.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r6y.ent.gz | 26.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r6y_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 1r6y_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 1r6y_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 1r6y_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/1r6y ftp://data.pdbj.org/pub/pdb/validation_reports/r6/1r6y | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12904.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Ammonium Sulphate, Tri-Sodium Citrate, Sodium/Potassium Tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. all: 9700 / Num. obs: 9700 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 | ||||||||||||||||||
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.944 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.2 / ESU R Free: 0.182 / 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: 37.566 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20 /
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