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Yorodumi- PDB-5mji: Crystal Structure of RosB with bound intermediate OHC-RP (8-demet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mji | ||||||
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Title | Crystal Structure of RosB with bound intermediate OHC-RP (8-demethyl-8-formylriboflavin-5'-phosphate) | ||||||
Components | BRAMP domain protein | ||||||
Keywords | FLAVOPROTEIN / Flavodoxin-like / roseoflavin / electron transport | ||||||
Function / homology | Function and homology information 8-demethyl-8-aminoriboflavin-5'-phosphate synthase / antibiotic metabolic process / transaminase activity / antibiotic biosynthetic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Streptomyces davawensis JCM 4913 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Konjik, V. / Bruenle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Mack, M. / Ermler, U. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: The Crystal Structure of RosB: Insights into the Reaction Mechanism of the First Member of a Family of Flavodoxin-like Enzymes. Authors: Konjik, V. / Brunle, S. / Demmer, U. / Vanselow, A. / Sandhoff, R. / Ermler, U. / Mack, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mji.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mji.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mji ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mji | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28899.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces davawensis JCM 4913 (bacteria) Gene: BN159_7989 / Production host: Escherichia coli (E. coli) / References: UniProt: K4REZ6 |
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#2: Chemical | ChemComp-7O6 / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion Details: 0.3 M sodium formate, 25 % (v/v) Silver Bullet 49, 17 % (v/v) PEG 3350 |
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 36244 / % possible obs: 99.9 % / Redundancy: 10.7 % / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 2.12 / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.806 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→46.806 Å
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Refine LS restraints |
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LS refinement shell |
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