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Yorodumi- PDB-6ui0: Artificial Iron Proteins: Modelling the Active Sites in Non-Heme ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ui0 | ||||||
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Title | Artificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases | ||||||
Components | Streptavidin | ||||||
Keywords | METAL BINDING PROTEIN / Biotin binding artificial metalloprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces avidinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.-S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. ...Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.-S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / Kern, J. / Yano, J. / Green, M.T. / Ward, T.R. / Borovik, A.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Inorg.Chem. / Year: 2020 Title: Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Authors: Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / ...Authors: Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / Kern, J. / Yano, J. / Green, M.T. / Ward, T.R. / Borovik, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ui0.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ui0.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ui0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ui0_validation.pdf.gz | 749.6 KB | Display | wwPDB validaton report |
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Full document | 6ui0_full_validation.pdf.gz | 752.3 KB | Display | |
Data in XML | 6ui0_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6ui0_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/6ui0 ftp://data.pdbj.org/pub/pdb/validation_reports/ui/6ui0 | HTTPS FTP |
-Related structure data
Related structure data | 6uiuC 6uiyC 6uizC 6us6C 2qcbS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: A) / NCS domain segments: (Refine code: 1 ) |
-Components
#1: Protein | Mass: 16552.965 Da / Num. of mol.: 1 / Mutation: K121A, E101Q, S112E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629 | ||||
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#2: Chemical | ChemComp-QFY / { | ||||
#3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-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: 47.36 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 26 mg/mL protein, 2.0 Ammonium Sulfate, 0.1 M sodium acetate pH 4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→37.45 Å / Num. obs: 31551 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.013 / Rrim(I) all: 0.066 / Net I/σ(I): 30.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCB Resolution: 1.4→37.45 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.846 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05 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: 86.95 Å2 / Biso mean: 21.554 Å2 / Biso min: 11.53 Å2
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Refinement step | Cycle: final / Resolution: 1.4→37.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 26 / Type: TIGHT THERMAL / Rms dev position: 0 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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