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Yorodumi- PDB-5w71: X-ray structure of BtrR from Bacillus circulans in the presence o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w71 | ||||||
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Title | X-ray structure of BtrR from Bacillus circulans in the presence of the 2-DOS external aldimine | ||||||
Components | L-glutamine:2-deoxy-scyllo-inosose aminotransferase | ||||||
Keywords | TRANSFERASE / butirosin / aminotransferase / aminoglycoside / aminocyclitol antibiotic | ||||||
Function / homology | Function and homology information L-glutamine:2-deoxy-scyllo-inosose aminotransferase / L-glutamine:3-amino-2,3-dideoxy-scyllo-inosose aminotransferase / polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Bacillus circulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2017 Title: The structure of RbmB from Streptomyces ribosidificus, an aminotransferase involved in the biosynthesis of ribostamycin. Authors: Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w71.cif.gz | 183.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w71.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 5w71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w71_validation.pdf.gz | 831.7 KB | Display | wwPDB validaton report |
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Full document | 5w71_full_validation.pdf.gz | 838.7 KB | Display | |
Data in XML | 5w71_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5w71_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/5w71 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/5w71 | HTTPS FTP |
-Related structure data
Related structure data | 5w70C 2c7tS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 49555.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Gene: btrR, btrS / Production host: Escherichia coli (E. coli) References: UniProt: Q8G8Y2, L-glutamine:2-deoxy-scyllo-inosose aminotransferase, L-glutamine:3-amino-2,3-dideoxy-scyllo-inosose aminotransferase #2: Chemical | ChemComp-PLP / | #3: Chemical | ChemComp-9YM / [ | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15-17% PEG-5000, 200 mM NaCl, 100 mM MOPS, 1 mM PLP, 5 mM 2-DOS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 14, 2016 / Details: montel |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 54841 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/av σ(I): 7.4 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6774 / Rsym value: 0.382 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2c7t Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.635 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.187 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.109 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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Refine LS restraints |
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