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Yorodumi- PDB-6cbn: x-ray structure of NeoB from streptomyces fradiae in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cbn | ||||||
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Title | x-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as the external aldimine) at pH 7.5 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 6cbn.cif.gz | 195.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cbn.ent.gz | 150.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cbn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6cbn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6cbn_validation.xml.gz | 40.8 KB | Display | |
Data in CIF | 6cbn_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/6cbn ftp://data.pdbj.org/pub/pdb/validation_reports/cb/6cbn | HTTPS FTP |
-Related structure data
Related structure data | 6cbkSC 6cblC 6cbmC 6cboC 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
#1: Protein | Mass: 47164.965 Da / Num. of mol.: 2 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 | #3: Chemical | ChemComp-EDO / | #4: 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: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18-20% PEG-5000, 200 mL LiCl, 100 mM HEPES, 1 mm PLP, 5 mM neomycin |
-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: Nov 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 181651 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.35→1.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 34033 / Rsym value: 0.393 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6cbk Resolution: 1.35→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.193 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.056 / 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: 15.11 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→50 Å
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Refine LS restraints |
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