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Yorodumi- PDB-5z8k: Crystal structure of an aminotransferase in complex with product-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z8k | |||||||||
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Title | Crystal structure of an aminotransferase in complex with product-1 | |||||||||
Components | C-6' aminotransferase | |||||||||
Keywords | TRANSFERASE / aminotransferase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Micromonospora echinospora (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.759 Å | |||||||||
Authors | Hong, S.K. / Cha, S.S. | |||||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat. Chem. Biol. / Year: 2019 Title: Complete reconstitution of the diverse pathways of gentamicin B biosynthesis. Authors: Ban, Y.H. / Song, M.C. / Hwang, J.Y. / Shin, H.L. / Kim, H.J. / Hong, S.K. / Lee, N.J. / Park, J.W. / Cha, S.S. / Liu, H.W. / Yoon, Y.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z8k.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z8k.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z8k_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5z8k_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5z8k_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 5z8k_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/5z8k ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z8k | HTTPS FTP |
-Related structure data
Related structure data | 5z83SC 5z8aC 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: 47174.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: gacK, genB1, gntW / Production host: Escherichia coli (E. coli) / References: UniProt: Q70KD9 #2: Chemical | #3: Sugar | #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: 2.31 Å3/Da / Density % sol: 46.69 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: magnesium formate, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.759→50 Å / Num. obs: 74626 / % possible obs: 92.2 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.023 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.299 / Num. unique obs: 2380 / Rpim(I) all: 0.143 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z83 Resolution: 1.759→32.298 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 21.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.13 Å2 / Biso mean: 20.3714 Å2 / Biso min: 6.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.759→32.298 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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