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Yorodumi- PDB-6k8h: Crystal structure of an omega-transaminase from Sphaerobacter the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k8h | |||||||||
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Title | Crystal structure of an omega-transaminase from Sphaerobacter thermophilus | |||||||||
Components | Aminotransferase class-III | |||||||||
Keywords | TRANSFERASE / Transaminase / Thermostability / Transamination | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Sphaerobacter thermophilus DSM 20745 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Park, H.H. / Kwon, S. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Structural insights into the enzyme specificity of a novel omega-transaminase from the thermophilic bacterium Sphaerobacter thermophilus. Authors: Kwon, S. / Lee, J.H. / Kim, C.M. / Ha, H.J. / Lee, S.H. / Lee, C.S. / Jeon, J.H. / So, I. / Park, H.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k8h.cif.gz | 199.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k8h.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/6k8h ftp://data.pdbj.org/pub/pdb/validation_reports/k8/6k8h | HTTPS FTP |
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-Related structure data
Related structure data | 4ao9S 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: 48685.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria) Strain: DSM 20745 / S 6022 / Gene: Sthe_0848 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D1C218 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate (pH 4.8), 1.2 M K2HPO4, 0.9 M NaH2PO4, 40% 2,5-hexanediol |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 63258 / % possible obs: 85.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 3017 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AO9 Resolution: 1.9→29.849 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 16.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.849 Å
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Refine LS restraints |
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LS refinement shell |
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