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Yorodumi- PDB-6uiu: Artificial Iron Proteins: Modelling the Active Sites in Non-Heme ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uiu | ||||||
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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 / molecular replacement / Resolution: 1.35 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 | 6uiu.cif.gz | 44.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uiu.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/6uiu ftp://data.pdbj.org/pub/pdb/validation_reports/ui/6uiu | HTTPS FTP |
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-Related structure data
Related structure data | 6ui0C 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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-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-QG7 / |
#3: 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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 26 mg/mL protein, 2.0 M 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: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→37.43 Å / Num. obs: 35163 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.067 / Rrim(I) all: 0.247 / Net I/σ(I): 5.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCB Resolution: 1.35→37.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 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: 81.21 Å2 / Biso mean: 16.164 Å2 / Biso min: 7.12 Å2
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Refinement step | Cycle: final / Resolution: 1.35→37.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.382 Å / Rfactor Rfree error: 0
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