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Yorodumi- PDB-6cbk: X-ray structure of NeoB from Streptomyces fradiae in complex with PMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cbk | ||||||
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Title | X-ray structure of NeoB from Streptomyces fradiae in complex with PMP | ||||||
Components | Neamine transaminase NeoN | ||||||
Keywords | TRANSFERASE / Neomycin / aminotransferase | ||||||
Function / homology | Function and homology information neamine transaminase / neomycin C transaminase / neomycin biosynthetic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Streptomyces fradiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Thoden, J.B. / Dow, G.T. / Holden, H.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2018 Title: The three-dimensional structure of NeoB: An aminotransferase involved in the biosynthesis of neomycin. Authors: Dow, G.T. / 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 | 6cbk.cif.gz | 339.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cbk.ent.gz | 276.4 KB | Display | PDB format |
PDBx/mmJSON format | 6cbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cbk_validation.pdf.gz | 489.1 KB | Display | wwPDB validaton report |
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Full document | 6cbk_full_validation.pdf.gz | 504 KB | Display | |
Data in XML | 6cbk_validation.xml.gz | 66.9 KB | Display | |
Data in CIF | 6cbk_validation.cif.gz | 96.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cbk ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cbk | HTTPS FTP |
-Related structure data
Related structure data | 6cblC 6cbmC 6cbnC 6cboSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45766.520 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: neoN, neo18, neoB / Production host: Escherichia coli (E. coli) References: UniProt: Q53U08, neamine transaminase, neomycin C transaminase #2: Chemical | ChemComp-PMP / #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-NA / | #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: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14-18% PEG-8000, 200 mM tetraethylammonium chloride, 200 mM HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→97.45 Å / Num. obs: 179314 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 17508 / Rsym value: 0.309 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CBO Resolution: 1.75→97.46 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.273 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.939 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→97.46 Å
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Refine LS restraints |
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